CN117136071A - Polypeptides and their use in the treatment of diseases - Google Patents

Polypeptides and their use in the treatment of diseases Download PDF

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CN117136071A
CN117136071A CN202280024873.9A CN202280024873A CN117136071A CN 117136071 A CN117136071 A CN 117136071A CN 202280024873 A CN202280024873 A CN 202280024873A CN 117136071 A CN117136071 A CN 117136071A
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amino acid
acid sequence
domain
polypeptide
antigen
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A·卡巴基比
A·S·哈米尔
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Wujing Co ltd
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Wujing Co ltd
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    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
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    • A61K39/4631—Chimeric Antigen Receptors [CAR]
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    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464402—Receptors, cell surface antigens or cell surface determinants
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    • A61K47/6849—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a receptor, a cell surface antigen or a cell surface determinant
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    • A61K47/6835—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site
    • A61K47/6851—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a determinant of a tumour cell
    • A61K47/6867—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a determinant of a tumour cell the tumour determinant being from a cell of a blood cancer
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    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
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    • C07K16/2851—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the lectin superfamily, e.g. CD23, CD72
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
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    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2863—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against receptors for growth factors, growth regulators
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
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    • A61K2239/10—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterized by the structure of the chimeric antigen receptor [CAR]
    • A61K2239/11—Antigen recognition domain
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    • A61K2239/48—Blood cells, e.g. leukemia or lymphoma
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    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
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    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
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    • C07K2317/622—Single chain antibody (scFv)
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    • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
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Abstract

Polypeptides, such as monoclonal antibodies (mabs) and functional fragments thereof, synthetic antigen binding proteins, such as single chain variable fragments (scFv), and Chimeric Antigen Receptors (CARs), that can specifically recognize tumor-associated antigens (TAAs) on cancer cells, such as those expressing CD33, FLT3, and CLL-1, are useful in the treatment of diseases, such as cancer.

Description

Polypeptides and their use in the treatment of diseases
Cross Reference to Related Applications
The present application claims priority and benefit from U.S. provisional patent application No. 63/148,012, filed on 10/2/2021, the entire contents of which are incorporated herein by reference.
Targeted immunotherapy is based on the recognition of antigens by immune receptors, which are defined structures on diseased cells or pathogens, which are soluble (i.e., antibodies) or CARs present on the surface of immune cells, such as immune effector cells (e.g., CAR-T cells) carrying Chimeric Antigen Receptors (CARs). Recognition and binding of antigens by immune receptors often trigger effector functions, ultimately leading to destruction of the corresponding pathogen or cell. Soluble immunoreceptors include natural or synthetic antibodies, antibody-derived molecules, and other structures that trigger the complement system or recruit and in most cases activate effector cells when bound to an antigen. Alternatively, antigen-targeted cells can be generated by genetically inserting an engineered immune receptor, such as a transgenic T Cell Receptor (TCR) or CAR, into T cells or other immune effector cells, including Natural Killer (NK) cells. Typically, a CAR comprises a single chain variable fragment (scFv) derived from an antibody specific for a certain target antigen, the scFv being coupled via a hinge region and a transmembrane region to a cytoplasmic domain of a T cell signaling molecule. CAR-mediated adoptive immunotherapy allows CAR-transplanted cells to directly recognize the desired antigen on target cells in a non-HLA-restricted manner.
One common application of these immunotherapies is the treatment of cancer, although it is not the only application. Cancer is a broad group of diseases involving deregulation of cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invading nearby body parts. Cancer may also spread to more distant sites in the body through the lymphatic system or blood flow. More than 200 different cancers are known in humans. Although good treatment options are available for many cancer types, there is still an unmet medical need for other cancer types.
Among these are hematological cancers. Cancers of the hematopoietic system can be broadly divided into different subtypes. Leukemia generally affects primary lymphoid organs (i.e., bone marrow and thymus) and originates from a hematopoietic progenitor cell population, such as, for example, acute Myeloid Leukemia (AML). Lymphoma, on the other hand, is usually derived from mature lymphocytes and from secondary lymphoid organs.
Currently, the first line treatment of most hematopoietic cancers involves administration of chemotherapeutic agents (broad spectrum or targeted therapies), radiation therapy, or a combination of both. In many cases, such therapies are combined with or followed by Hematopoietic Stem Cell Transfer (HSCT), where graft versus leukemia (GvL) effects mediated by donor-derived lymphocytes, especially T cells, can promote eradication of cancer cells that survive preconditioning chemotherapy or radiation therapy and achieve Complete Remission (CR). Various forms of HSCT are routinely performed clinically, depending on the type of hematologic malignancy, the condition of the patient, and the availability of hematopoietic stem cell grafts. Currently, the desired GvL effect is only achieved in allogeneic HSCT, while often accompanied by the occurrence of graft versus host disease (GvHD), a serious and sometimes fatal complication. Furthermore, in all cases, the continued presence of cancer stem cells often leads to recurrence of the disease.
In recent years, there has been great progress in the development of targeted immunotherapy (e.g., CAR-T cells) for the treatment of cancer. However, most targeted immunotherapy broadly targets antigens expressed on malignant and healthy cells, and uses polypeptides that target antigens in a polymorphic non-selective manner. In addition, the recurrence of hematological cancer in patients with HSCT transplants remains a problem to be solved. Thus, there is a need to develop novel therapies for treating diseases (such as cancer) that can utilize alternative target molecules and reduce or avoid side effects typically associated with currently common targeted immunotherapy, particularly CAR T cell therapies.
Disclosure of Invention
Provided herein are polymorphic selective polypeptides, including single chain variable fragments, monoclonal antibodies and antigen binding fragments thereof, antibody-drug conjugates, and chimeric antigen receptors, as well as engineered immune effector cells comprising the same, which are useful in the treatment of diseases (such as cancer), and in some embodiments, are combined with polymorphic mismatched hematopoietic cell grafts in a manner that allows selective killing of diseased cells in a patient while retaining transplanted hematopoietic cells.
Brief description of the sequence
SEQ ID NOS 1 to 200: the CDRs of polymorphic, selective anti-CD 33 polypeptides 1-25 and the sequences of the VH and VL chains.
SEQ ID NOS 201 to 336: the CDRs of polymorphic, selective anti-CD 33 polypeptide 26-42 and the sequences of the VH and VL chains.
SEQ ID NOS: 337 to 528: the CDRs of polymorphic, selective anti-CLL-1 polypeptide 43-66, and the sequences of the VH and VL chains.
529 to 704: the CDRs of polymorphic, selective anti-CLL-1 polypeptide 67-88, and the sequences of the VH and VL chains.
SEQ ID NOS 705-1144 and 1979-2002: the CDRs of polymorphic non-selective anti-CD 33 polypeptides 89-143 and 191-193 and the sequences of the VH and VL chains.
SEQ ID NOS: 1145-1520 and 2003-2058: the CDRs of polymorphic non-selective anti-CLL-1 polypeptides 144-190 and 194-200 and the sequences of the VH and VL chains.
SEQ ID NOS: 1521 to 1538: amino acid sequence of the CAR component selected.
SEQ ID NOS 1539 to 1598: the sequences of exemplary CARs can be prepared using the polypeptides disclosed herein.
SEQ ID NOS 1599 to 1626: a human antibody Fc component that can be combined with a polypeptide disclosed herein to form a diagnostic or therapeutic antibody.
SEQ ID NO. 1627-1802: exemplary anti-CD 33 and anti-CLL-1 IgG1 antibody sequences comprising polypeptides 1-88.
SEQ ID NOS 1803 to 1978: exemplary anti-CD 33 and anti-CLL-1 IgG4 antibody sequences comprising polypeptides 1-88.
SEQ ID NOS 2059 to 2810: the CDRs of polymorphic non-selective anti-FLT 3 polypeptides 201-294 and the sequences of the VH and VL chains.
Drawings
FIG. 1 shows the CD33 extracellular domain (ECD) with Amino Acid (AA) 69 in the left panel and FLT3 ECD AA267 in the right panel each in a relative solvent accessible position.
FIG. 2 shows control (C) parental Jurkat cells, jurkat cells expressing CD33-R69 (R69), and Jurkat cells expressing CD33-G69 (G69), and they were treated as follows:
a: PD-L1 scFv as a negative control, which resulted in mean fold intensity changes of R69 and G69 relative to the parental cells of 0.73 and 0.66, respectively;
b: CD33 non-selective scFv as a positive control, which resulted in MFI changes of R69 and G69 relative to the parent cell of 78.9 and 74.6, respectively;
c: CD33-R69 selective scFv resulting in MFI changes of R69 and G69 of 20.3 and 0.58, respectively, relative to the parent cell; and
d: CD33-G69 selective scFv, which resulted in MFI changes of R69 and G69 relative to the parent cell of 0.59 and 45.9, respectively.
FIG. 3 shows the fold selectivity of polypeptides 1-42 for huCD33-R69 or huCD33-G69 stably expressed in Jurkat cells.
FIG. 4 shows the results of an in vitro cytotoxicity assay using CART33 ARG69 、CART33 GLY69 Or CART33 treatment of CD33 GLY69 A culture of a cellular target. CART33 GLY69 And CART33 effectively kills expressed CD33 GLY69 But CART33 ARG69 This is not the case.
FIG. 5 shows the results of an in vitro cytotoxicity assay with CART33 ARG69 、CART33 GLY69 Or CART33 treatment of CD33 ARG69 A culture of a cellular target. CART33 ARG69 And CART33 effectively kills expressed CD33 ARG69 But CART33 GLY69 This is not the case.
Detailed Description
Provided herein are polymorphic selective polypeptides, including single chain variable fragments, monoclonal antibodies and antigen binding fragments thereof, antibody-drug conjugates, and chimeric antigen receptors, as well as engineered immune effector cells comprising the same, which are useful in the treatment of diseases (such as cancer), and in some embodiments, are combined with polymorphic mismatched hematopoietic cell grafts in a manner that allows selective killing of diseased cells in a patient while retaining transplanted hematopoietic cells.
Examples
Thus, while other embodiments can be found throughout the disclosure, the following embodiments are provided herein:
example 1. A polypeptide that selectively binds to a first polymorphic variant of a human cancer cell antigen relative to a second polymorphic variant of the human cancer cell antigen; or a second polymorphic variant that selectively binds to the antigen relative to the first polymorphic variant of the antigen.
Example 2. The polypeptide of example 1, wherein the antigen is selected from the group consisting of CD33, CLL-1, and FLT3.
Example 3. The polypeptide of example 2, wherein the antigen is CD33.
Example 4. A polypeptide that selectively binds to a first polymorphic variant of CD33 relative to a second polymorphic variant of CD 33; or a second polymorphic variant that selectively binds to the CD33 relative to the first polymorphic variant of the CD 33; wherein the binding has a selectivity of at least 2-fold.
Embodiment 5. The polypeptide of embodiment 4, wherein the binding has a selectivity of at least 10-fold.
Example 6. The polypeptide of example 5, wherein the binding has a selectivity of at least 30-fold.
Embodiment 7 the polypeptide of any one of embodiments 3-6, wherein the first polymorphic variant of CD33 is R69 and the second polymorphic variant of CD33 is G69; or the first polymorphic variant of CD33 is G69 and the second polymorphic variant of CD33 is R69.
Example 8. The polypeptide of example 7, comprising six Complementarity Determining Regions (CDRs).
Example 9. The polypeptide of example 8, comprising:
three heavy chain variable (V H ) Domain CDR: HCDR1, HCDR2 and HCDR3; and
Three light chain variable (V L ) Domain CDR: LCDR1, LCDR2, and LCDR3.
Embodiment 10. The polypeptide of any one of embodiments 7-9, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1-25 and 201-217,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 26-50 and 218-234,
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 51-75 and 235-251.
Embodiment 11. The polypeptide of any one of embodiments 7-9, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1-25,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 26-50, and
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 51-75.
Embodiment 12. The polypeptide of any one of embodiments 7-9, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 201-217,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 218-234, and
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 235-251.
Embodiment 13. The polypeptide of any one of embodiments 10-12, wherein the HCDR1, HCDR2 and HCDR3 have at least 97%, 98% or 99% sequence identity to one of the amino acid sequences.
Embodiment 14. The polypeptide of any one of embodiments 10-12, wherein the HCDR1, HCDR2 and HCDR3 have the amino acid sequence.
Embodiment 15. The polypeptide of any one of embodiments 7-9 and 8-14, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 76-100 and 252-268,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 101-125 and 269-285, and
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 126-150 and 286-302.
Embodiment 16. The polypeptide of any one of embodiments 7-9 and 8-14, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 76-100,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 101-125, and
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 126-150.
Embodiment 17 the polypeptide of any one of embodiments 7-9 and 8-14, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 252-268,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 269-285, and
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 286-302.
Embodiment 18. The polypeptide of any one of embodiments 15-17, wherein the LCDR1, LCDR2, and LCDR3 have at least 97%, 98%, or 99% sequence identity with one of the amino acid sequences.
Embodiment 19. The polypeptide of any one of embodiments 15-17, wherein the LCDR1, LCDR2, and LCDR3 have the amino acid sequence.
Example 20 the polypeptide of example 7 comprising V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 151-175 and 303-319.
Example 21 the polypeptide of example 7 comprising V H Domain of V H The domain having a sequence selected from any one of SEQ ID NOS 151-175 exhibitsAmino acid sequence of at least 95% sequence identity.
Example 22 the polypeptide of example 7 comprising V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 303-319.
Embodiment 23 the polypeptide of any one of embodiments 20-22, wherein the V H The domain has at least 97%, 98% or 99% sequence identity to one of the amino acid sequences.
Embodiment 24 the polypeptide of any one of embodiments 20-22, wherein the V H The domain has one of the amino acid sequences.
Embodiment 25 the polypeptide of any one of embodiments 7 and 20-24 comprising V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 176-200 and 320-336.
Embodiment 26 the polypeptide of any one of embodiments 7 and 20-24 comprising V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 176-200.
Embodiment 27 the polypeptide of any one of embodiments 7 and 20-24, comprising V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 320-336.
Embodiment 28 the polypeptide of any one of embodiments 25-27, wherein the V L The domain has at least 97%, 98% or 99% sequence identity to one of the amino acid sequences.
Embodiment 29 the polypeptide of any one of embodiments 25-27, wherein the V L The domain has one of the amino acid sequences.
Embodiment 30 the polypeptide of any one of embodiments 20-29, comprising V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 1-42.
Embodiment 31 the polypeptide of any one of embodiments 20-29, comprising V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 1-25.
Embodiment 32 the polypeptide of any one of embodiments 20-29, comprising V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 26-42.
Embodiment 33 the polypeptide of any one of embodiments 30-33, wherein the V H Domain and the V L The domain has at least 97%, 98% or 99% sequence identity to one of the pair of amino acid sequences.
Embodiment 34. The polypeptide of embodiment 2, wherein the antigen is FLT3.
Example 35. A polypeptide that selectively binds to a first polymorphic variant of FLT3 relative to a second polymorphic variant of FLT 3; or a second polymorphic variant that selectively binds to the FLT3 relative to the first polymorphic variant; wherein the binding has a selectivity of at least 2-fold.
Embodiment 36. The polypeptide of embodiment 35, wherein the binding has at least 10-fold selectivity.
Embodiment 37. The polypeptide of embodiment 36, wherein the binding has a selectivity of at least 30-fold.
Embodiment 38 the polypeptide of any one of embodiments 34-37, wherein the first polymorphic variant of FLT3 is T227 and the second polymorphic variant of FLT3 is M227; or the first polymorphic variant of FLT3 is M227 and the second polymorphic variant of FLT3 is T227.
Example 39 the polypeptide of example 2, wherein the antigen is CLL-1.
Example 40. A polypeptide that selectively binds to a first polymorphic variant of CLL-1 relative to a second polymorphic variant of CLL-1; or a second polymorphic variant that selectively binds to CLL-1 relative to the first polymorphic variant; wherein the binding has a selectivity of at least 2-fold.
Embodiment 41. The polypeptide of embodiment 40, wherein the binding has at least 10-fold selectivity.
Embodiment 42. The polypeptide of embodiment 40, wherein the binding has a selectivity of at least 30-fold.
Embodiment 43 the polypeptide of any one of embodiments 39-42, wherein the first polymorphic variant of CLL-1 is K224 and the second polymorphic variant of CLL-1 is Q244; or the first polymorphic variant of CLL-1 is Q224 and the second polymorphic variant of CLL-1 is K244.
The polypeptide of claim 43, wherein the polypeptide comprises six Complementarity Determining Regions (CDRs).
Example 45 the polypeptide of example 44, comprising:
three heavy chain variable (V H ) Domain CDR: HCDR1, HCDR2 and HCDR3; and
three light chain variable (V L ) Domain CDR: LCDR1, LCDR2, and LCDR3.
Embodiment 46. The polypeptide of any one of embodiments 43-45, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 337-360 and 529-550,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 361-384 and 551-572, an
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 385-408 and 573-594.
Embodiment 47. The polypeptide of any one of embodiments 43-45, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 337-360,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 361-384, an
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 385-408.
Embodiment 48 the polypeptide of any one of embodiments 43-45, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 529-550,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 551-572, and
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 573-594.
Embodiment 49 the polypeptide of any one of embodiments 46-48, wherein the HCDR1, HCDR2 and HCDR3 have at least 97%, 98% or 99% sequence identity to one of the amino acid sequences.
Embodiment 50. The polypeptide of any one of embodiments 46-48, wherein the HCDR1, HCDR2 and HCDR3 have the amino acid sequence.
Embodiment 51 the polypeptide of any one of embodiments 43-50, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 409-432 and 595-616,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 433-456 and 617-638, and
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 457-480 and 639-660.
Embodiment 52 the polypeptide of any one of embodiments 43-50, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS 409-432,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 433-456, an
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 457-480.
Embodiment 53 the polypeptide of any one of embodiments 43-50, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NO:595-616,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 617-638, an
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 639-660.
Embodiment 54 the polypeptide of any one of embodiments 51-53, wherein the LCDR1, LCDR2 and LCDR3 have at least 97%, 98% or 99% sequence identity with one of said amino acid sequences.
Embodiment 55. The polypeptide of any one of embodiments 51-53, wherein the LCDR1, LCDR2 and LCDR3 have the amino acid sequence.
Example 56 the polypeptide of example 44 comprising V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 151-175 and 303-319.
Example 57 the polypeptide of example 44 comprising V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 151-175.
Example 58 the polypeptide of example 44, which comprises V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 303-319.
Embodiment 59 the polypeptide of any one of embodiments 56-58, wherein the V H The domain has at least 97%, 98% or 99% sequence identity to one of the amino acid sequences.
Embodiment 60 the polypeptide of any one of embodiments 56-58, wherein the V H The domain has the amino acid sequenceIs a member of the group consisting of a metal, a metal alloy.
Embodiment 61 the polypeptide of any one of embodiments 44 and 56-60 comprising V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 176-200 and 320-336.
Embodiment 62 the polypeptide of any one of embodiments 44 and 56-60, which comprises V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 176-200.
Embodiment 63 the polypeptide of any one of embodiments 44 and 56-60, which comprises V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 320-336.
Embodiment 64 the polypeptide of any one of embodiments 61-63, wherein the V L The domain has at least 97%, 98% or 99% sequence identity to one of the amino acid sequences.
Embodiment 65 the polypeptide of any one of embodiments 61-63, wherein the V L The domain has one of the amino acid sequences.
Example 66 the polypeptide of any one of examples 56-65, which comprises V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 43-88.
Embodiment 67 the polypeptide of any one of embodiments 56-65, which comprises V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 43-66.
Embodiment 68 the polypeptide of any one of embodiments 56-65, which comprises V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 67-88.
Embodiment 69 the polypeptide of any one of embodiments 66-68, wherein the V H Domain and the V L The domain has at least 97%, 98% or 99% sequence identity to one of the pair of amino acid sequences.
Example 70. A single chain variable fragment (scFv) comprising the polypeptide of any one of examples 1-69.
Example 71 a monoclonal antibody (mAb) or antigen-binding fragment thereof comprising the polypeptide of any one of examples 1-69.
Example 72. The mAb of example 71, or an antigen-binding fragment thereof, wherein the mAb is of an IgG, igM, or IgA isotype.
Example 73. The mAb of example 72, or an antigen-binding fragment thereof, wherein the mAb is of the IgG1 isotype.
Example 74. The mAb of example 72, or an antigen-binding fragment thereof, wherein the mAb is of the IgG3 isotype.
Example 75. The mAb of example 72, or antigen-binding fragment thereof, wherein the mAb is of the IgG4 isotype.
Example 76 the mAb of example 72, or antigen-binding fragment thereof, wherein the mAb is human or humanized.
Embodiment 77. The mAb of any one of embodiments 71-76, or an antigen binding fragment thereof, wherein said mAb comprises a sequence selected from the group consisting of SEQ ID NOS 1201-1368.
Embodiment 78 an antibody-drug conjugate (ADC) comprising the mAb or antigen-binding fragment thereof of any one of embodiments 71-77.
Embodiment 79. The ADC of embodiment 52, having formula I:
Ab-(L-D) p
(I)
wherein:
ab is an antibody comprising the polypeptide of any one of embodiments 1-43, or the antibody of any one of embodiments 45-51, or an antigen-binding fragment of either of the foregoing;
l is a linker;
d is a drug; and is also provided with
p is from about 1 to about 20.
Embodiment 80. The ADC of embodiment 79, wherein D is selected from saporin, MMAE, MMAF, DM, and DM4.
Example 81 a Chimeric Antigen Receptor (CAR) comprising an extracellular ligand binding domain comprising the polypeptide of any one of examples 1-69.
Embodiment 82. The CAR of embodiment 81, further comprising:
a hinge domain;
a transmembrane domain;
optionally, one or more co-stimulatory domains; and
cytoplasmic signaling domains.
Example 83 the CAR of example 82, wherein the hinge domain is selected from fceriia, CD8 a, CD28, and IgG1.
Embodiment 84. The CAR of embodiment 83, wherein the hinge domain is CD8 a.
Embodiment 85 the CAR of any one of embodiments 82-84, wherein the transmembrane domain is selected from the group consisting of the alpha, beta, or zeta chain of the T cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD9, CD16, CD22, CD33, CD37, CD64, CDs0, CD86, CD134, CD137, and CD154.
Embodiment 86. The CAR of embodiment 85, wherein the transmembrane domain is CD28.
Embodiment 87. The CAR of any of embodiments 82-86, wherein the cytoplasmic signaling domain is selected from the group consisting of CD8, cd3ζ, cd3δ, cd3γ, cd3ε, CD22, CD32, DAP10, DAP12, CD66d, CD79a, CD79b, fcyriγ, fcrγ, fcrβ, and fcrepsilon.
Example 88 the CAR of example 87, wherein the cytoplasmic signaling domain is CD3 zeta.
Embodiment 89 the CAR of any of embodiments 82-88, wherein one co-stimulatory domain is selected from the group consisting of 4-1BB, CD28, and ICOS.
Example 90 the CAR of example 89, wherein the co-stimulatory domain is CD28.
Example 91 the CAR of example 89, wherein the co-stimulatory domain is 4-1BB.
Example 92. The CAR of example 89, comprising two or more co-stimulatory domains.
Example 93. The CAR of example 89, wherein two of the co-stimulatory domains are CD28 and 4-1BB.
Example 94 the CAR of example 82, comprising a sequence selected from SEQ ID NOs 1539-1598.
Example 95. A nucleotide sequence encoding the polypeptide, scFv, mAb or CAR of any one of examples 1-94.
Example 96. A vector comprising the nucleotide sequence set forth in example 95.
Embodiment 97. The vector of embodiment 96, wherein the vector is a lentiviral vector.
Example 98 the vector of example 97, wherein the lentiviral vector comprises a VSVG domain.
Example 99. An engineered immune effector cell that expresses the CAR of any one of examples 81-94 on the surface of the cell.
Example 100. The engineered immune effector cell of example 99, wherein the engineered immune effector cell expresses on the surface of the cell:
a first polymorphic variant of a human cancer cell antigen; and
a CAR that is selective for a second polymorphic variant relative to a first polymorphic variant of the antigen.
Example 101. The engineered immune effector cell of example 99, wherein the cell is a primary cell.
Example 102. The engineered immune effector cell of example 99, wherein the cell is derived from:
induced pluripotent stem cells (ipscs);
cord blood;
peripheral blood; or alternatively
Immortalized cell lines.
Example 103. The engineered immune effector cell of example 102, wherein the immortalized cell line is NK-92.
Embodiment 104. The engineered immune cell of any one of embodiments 99-103, wherein the cell is selected from the group consisting of a T cell, a Natural Killer (NK) cell, a constant natural killer T (iNKT) cell, a macrophage, and a dendritic cell.
Example 105. The engineered immune effector cell of example 104, wherein the cell is a T cell.
Embodiment 106. The engineered immune effector cell of embodiment 105, wherein the T cell is selected from the group consisting of an inflammatory T-lymphocyte, a cytotoxic T-lymphocyte, a regulatory T-lymphocyte, or a helper T-lymphocyte.
Example 107. The engineered immune effector cell of example 105, wherein the engineered immune effector cell lacks subunits of the T cell receptor complex.
Example 108. The engineered immune effector cell of example 107, wherein the subunit of the T cell receptor complex is selected from the group consisting of Tcra (TRAC), tcrp, tcrδ, tcrγ, cd3ε, cd3γ, cd3δ, and cd3ζ.
Embodiment 109. The engineered immune effector cell of any one of embodiments 99-108, wherein the engineered immune effector cell lacks a cell surface protein that is a target of the CAR.
Embodiment 110. The engineered immune effector cell of embodiment 104, wherein the engineered immune effector cell is an NK cell.
Example 111 the engineered immune effector cell of example 110, wherein the engineered immune effector cell is a memory-like (ML) NK cell.
Embodiment 112. The engineered immune effector cell of embodiment 111, wherein the engineered immune effector cell is a cytokine-induced memory-like (CIML) NK cell.
Example 113. The engineered immune effector cell of example 104, wherein the engineered immune effector cell is an iNKT cell.
Example 114. A method of treating a subject in need thereof, the subject having a first polymorphic variant of an antigen on the surface of a target cell, the method comprising:
a. optionally, treating the subject with one or more conditioning regimens to deplete target cells of the subject carrying the first polymorphic variant of the antigen;
b. administering to the subject:
-an engineered population of immune effector cells expressing a Chimeric Antigen Receptor (CAR) that selectively binds a first polymorphic variant of the antigen on the surface of the target cell; or alternatively
-a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell; or alternatively
-an antibody-drug conjugate (ADC) comprising a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell; and
c. administering to the subject a population of donor hematopoietic cells, a plurality of which comprise a second polymorphic variant of the antigen;
wherein administration of the hematopoietic cells and administration of the CAR-expressing cells, mAb, or ADC may be performed simultaneously, or sequentially in either order.
Example 115. A method of immunotherapy of a human subject in need thereof, the subject having a first polymorphic variant of an antigen on the surface of a target cell, the method comprising:
a. optionally, treating the subject with one or more conditioning regimens to deplete target cells of the subject carrying the first polymorphic variant of the antigen;
b. Administering to the subject a population of donor hematopoietic cells, a plurality of which comprise a second polymorphic variant of the antigen; and
c. administering to the subject:
-an engineered population of immune effector cells expressing a Chimeric Antigen Receptor (CAR) that specifically binds a first polymorphic variant of the antigen on the surface of a target cell; or alternatively
-a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell; or alternatively
-an antibody-drug conjugate (ADC) comprising a monoclonal antibody (mAb) or antigen-binding fragment thereof, which mAb or antigen-binding fragment thereof selectively binds to a first polymorphic variant of the antigen on the surface of the target cell.
Example 116. A method of treating a subject in need thereof, the subject having a first polymorphic variant of an antigen on the surface of a target cell, the method comprising:
a. administering to the subject:
-an engineered population of immune effector cells expressing a Chimeric Antigen Receptor (CAR) that binds to the antigen on the surface of the target cell; or alternatively
-a monoclonal antibody (mAb) that binds to the antigen on the surface of the target cell; or alternatively
-an antibody-drug conjugate (ADC) comprising a monoclonal antibody (mAb) that binds to the antigen on the surface of the target cell; and
b. optionally, treating the subject with one or more conditioning regimens to deplete target cells of the subject carrying the first polymorphic variant of the antigen;
c. administering to the subject:
-an engineered population of immune effector cells expressing a Chimeric Antigen Receptor (CAR) that selectively binds a first polymorphic variant of the antigen on the surface of the target cell; or alternatively
-a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell; or alternatively
-an antibody-drug conjugate (ADC) comprising a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell; and
d. administering to the subject a population of donor hematopoietic cells, a plurality of which comprise a second polymorphic variant of the antigen;
wherein administration of the hematopoietic cells and administration of the CAR-expressing cells, mAb, or ADC may be performed simultaneously, or sequentially in either order.
Embodiment 117 the method of any of embodiments 114-116, wherein the subject is a human.
Embodiment 118 the method of any one of embodiments 114-117, wherein the binding has a selectivity of at least 2-fold.
Embodiment 119. The method of embodiment 118, wherein the binding has a selectivity of at least 10-fold.
Embodiment 120 the method of embodiment 119, wherein the binding has a selectivity of at least 30-fold.
Embodiment 121 the method of any one of embodiments 114-120, wherein the antigen is selected from the group consisting of CD33, CLL-1, and FLT3.
Example 122 the method of example 121, wherein the antigen is CD33.
Embodiment 123 the method of embodiment 122, wherein the first polymorphic variant of CD33 is R69 and the second polymorphic variant of CD33 is G69; or the first polymorphic variant of CD33 is G69 and the second polymorphic variant of CD33 is R69.
Embodiment 124 the method of embodiment 121, wherein the antigen is FLT3.
Embodiment 125 the method of embodiment 124, wherein the first polymorphic variant of FLT3 is T227 and the second polymorphic variant of FLT3 is M227; or the first polymorphic variant of FLT3 is M227 and the second polymorphic variant of FLT3 is T227.
Embodiment 126. The method of embodiment 121, wherein the antigen is CLL-1.
Embodiment 127 the method of embodiment 126, wherein the first polymorphic variant of CLL-1 is K224 and the second polymorphic variant of CLL-1 is Q244; or the first polymorphic variant of CLL-1 is Q224 and the second polymorphic variant of CLL-1 is K244.
Embodiment 128 the method of any one of embodiments 114-127, wherein the subject is administered both the engineered immune effector cell population and the hematopoietic cell population simultaneously.
Embodiment 128 the method of any one of embodiments 114-127, wherein the hematopoietic cell population, and the engineered immune effector cell population, mAb, or ADC are sequentially administered to the subject.
Embodiment 130 the method of any one of embodiments 114-127, wherein the population of engineered immune effector cells, mAb or ADC, and the population of hematopoietic cells are sequentially administered to the subject.
Embodiment 131 the method of any one of embodiments 114-130, wherein prior to administering the hematopoietic cells, the subject is treated with one or more conditioning protocols to deplete the subject of target cells bearing the first polymorphic variant of the antigen.
The method of any of examples 114-130, wherein the subject has been conditioned with one or more conditioning protocols to deplete target cells of the subject that carry the first polymorphic variant of the antigen.
Embodiment 133 the method of any one of embodiments 114-12, wherein the hematopoietic cells are hematopoietic stem cells and/or hematopoietic progenitor cells.
Embodiment 134 the method of any of embodiments 114-133, wherein the subject is administered an engineered population of immune effector cells expressing a Chimeric Antigen Receptor (CAR) that selectively binds a first polymorphic variant of the antigen on the surface of the target cell.
Embodiment 135 the method of embodiment 134, wherein the engineered immune effector cells are derived from the subject (i.e., autologous) and the hematopoietic cells are derived from a donor (i.e., allogeneic).
Example 136 the method of example 134, wherein the engineered immune effector cells and hematopoietic cells are derived from a single donor.
Embodiment 137 the method of embodiment 134, wherein the engineered immune effector cells are derived from a first donor and the hematopoietic cells are derived from a second donor.
Embodiment 138 the method of any one of embodiments 134-137, wherein the Chimeric Antigen Receptor (CAR) comprises the polypeptide of any one of embodiments 1-69.
The method of any of embodiments 134-137, wherein the Chimeric Antigen Receptor (CAR) comprises an scFv as set forth in embodiment 70.
Embodiment 140 the method of any of embodiments 134-137, wherein the Chimeric Antigen Receptor (CAR) is the CAR of any of embodiments 81-94.
Embodiment 141 the method of any one of embodiments 134-137, wherein the engineered immune effector cell is an engineered immune effector cell of any one of embodiments 99-113.
The method of any one of embodiments 114-133, wherein a monoclonal antibody (mAb) or antigen-binding fragment thereof is administered to the subject, which mAb or antigen-binding fragment thereof selectively binds to a first polymorphic variant of the antigen on the surface of the target cell.
Embodiment 143. The method of embodiment 142, wherein the monoclonal antibody (mAb) comprises a polypeptide of any one of embodiments 1-69.
Example 144 the method of example 116, wherein the monoclonal antibody (mAb) is a mAb as described in any one of examples 71-77.
Embodiment 145 the method of any of embodiments 114-133, wherein an antibody-drug conjugate (ADC) comprising a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell is administered to the subject.
Embodiment 146 the method of any one of embodiments 142-145, wherein the mAb or ADC is administered prophylactically after transplantation to prevent relapse.
Embodiment 147 the method of any of embodiments 114-146, further comprising genotyping the subject and donor to ensure that the HSC donor and patient express different variants of the target antigen.
Example 148 the method of example 147, wherein the genotyping is performed using a protein-based assay (FACS) or a DNA-based assay (PCR).
Example 149 the method of example 147, wherein the patient is genotyped after a recurrence of the transplant.
Example 150 the method of example 147, wherein the patient is genotyped prior to transplantation.
Embodiment 151. The method of embodiment 147, wherein the hematopoietic cell donor is genotyped prior to hematopoietic cell transplantation.
Embodiment 152 the method of any one of embodiments 137-147, wherein the immune effector cell donor is genotyped prior to transplanting the population of engineered immune effector cells expressing the CAR.
Embodiment 153 the method of any one of embodiments 137-147, wherein the immune effector cell donor is genotyped prior to hematopoietic cell transplantation.
Example 154 a polypeptide that binds CD33 comprising:
three heavy chain variable (V H ) Domain CDR: HCDR1, HCDR2 and HCDR3; and/or
Three light chain variable (V L ) Domain CDR: LCDR1, LCDR2, and LCDR3; wherein the method comprises the steps of
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 705-7559 and 1979-1981;
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 760-814 and 1982-1984;
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 815-869 and 1985-1987;
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 870-924 and 1988-1990;
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 925-979 and 1991-1993; and is also provided with
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 980-1034 and 1994-1996.
Example 155 the polypeptide of example 154, comprising a combination of HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, selected from the group consisting of:
705, 760, 815, 870, 925, and 980;
706, 761, 816, 871, 926, and 981;
707, 762, 817, 872, 927, and 982;
708, 763, 818, 873, 928 and 983;
709, 764, 819, 874, 929, and 984;
710, 765, 820, 875, 930, and 985;
711, 766, 821, 876, 931, and 986;
712, 767, 822, 877, 932 and 987;
713, 768, 823, 878, 933 and 988;
714, 769, 824, 879, 934 and 989;
715, 770, 825, 880, 935 and 990;
716, 771, 826, 881, 936, and 991;
717, 772, 827, 882, 937 and 992;
718, 773, 828, 883, 938, and 993;
719, 774, 829, 884, 939, and 994;
720, 775, 830, 885, 940, and 995;
721, 776, 831, 886, 941, and 996;
722, 777, 832, 887, 942, and 997;
723, 778, 833, 888, 943 and 998;
724, 779, 834, 889, 944, and 999;
725, 780, 835, 890, 945 and 1000;
726, 781, 836, 891, 946, and 1001;
727, 782, 837, 892, 947 and 1002;
728, 783, 838, 893, 948, and 1003;
729, 784, 839, 894, 949 and 1004;
730, 785, 840, 895, 950, and 1005;
731, 786, 841, 896, 951, and 1006;
732, 787, 842, 897, 952, and 1007;
733, 788, 843, 898, 953, and 1008;
734, 789, 844, 899, 954 and 1009;
735, 790, 845, 900, 955 and 1010;
736, 791, 846, 901, 956, and 1011;
737, 792, 847, 902, 957, and 1012;
738, 793, 848, 903, 958, and 1013;
739, 794, 849, 904, 959, and 1014;
740, 795, 850, 905, 960, and 1015;
741, 796, 851, 906, 961 and 1016;
742, 797, 852, 907, 962 and 1017;
743, 798, 853, 908, 963 and 1018;
744, 799, 854, 909, 964, and 1019;
745, 800, 855, 910, 965 and 1020;
746, 801, 856, 911, 966 and 1021;
747, 802, 857, 912, 967 and 1022;
748, 803, 858, 913, 968, and 1023;
749, 804, 859, 914, 969 and 1024;
750, 805, 860, 915, 970, and 1025;
751, 806, 861, 916, 971, and 1026;
752, 807, 862, 917, 972 and 1027;
753, 808, 863, 918, 973, and 1028;
754, 809, 864, 919, 974, and 1029;
755, 810, 865, 920, 975, and 1030;
756, 811, 866, 921, 976 and 1031;
757, 812, 867, 922, 977, and 1032;
758, 813, 868, 923, 978, and 1033;
759, 814, 869, 924, 979, and 1034;
1979, 1982, 1985, 1988, 1991 and 1994;
SEQ ID NO. 1980, 1983, 1986, 1989, 1992 and 1995; and
SEQ ID NO. 1981, 1984, 1987, 1990, 1993 and 1996;
or a combination of HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3 having at least 95% sequence identity with each of the foregoing.
Example 156 the polypeptide of example 154, which comprises V H Domain and V L Domain, wherein:
the V is H The domain comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1035-1089 and 1997-1999; and/or
The V is L The domain comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 1090-1144 and 2000-2002.
Example 157 the polypeptide of example 156 comprising V selected from H Domain and V L Combination of domains:
1035 and 1090;
1036 and 1091;
1037 and 1092;
1038 and 1093;
1039 and 1094;
1040 and 1095;
1041 and 1096;
1042 and 1097;
1043 and 1098;
1044 and 1099;
1045 and 1100;
1046 and 1101;
1047 and 1102;
1048 and 1103;
1049 and 1104;
1050 and 1105;
1051 and 1106;
1052 and 1107;
1053 and 1108;
1054 and 1109;
1055 and 1110;
1056 and 1111;
1057 and 1112;
1058 and 1113;
1059 and 1114;
1060 and 1115;
SEQ ID NOS 1061 and 1116;
1062 and 1117;
SEQ ID NOs 1063 and 1118;
1064 and 1119;
1065 and 1120;
1066 and 1121;
1067 and 1122;
1068 and 1123;
SEQ ID NOs 1069 and 1124;
1070 and 1125;
1071 and 1126;
1072 and 1127;
1073 and 1128;
1074 and 1129;
1075 and 1130;
1076 and 1131;
1077 and 1132;
1078 and 1133;
1079 and 1134;
1080 and 1135;
1081 and 1136;
1082 and 1137;
1083 and 1138;
1084 and 1139;
1085 and 1140;
1086 and 1141;
1087 and 1142;
1088 and 1143;
1089 and 1144;
SEQ ID NOS.1997 and 2000;
SEQ ID NOS.1998 and 2001; and
1999 and 2002;
or V having at least 95% sequence identity to the preceding H Domain and V L Combinations of domains.
Example 158. A polypeptide that binds CLL-1, the polypeptide comprising:
three heavy chain variable (V H ) Domain CDR: HCDR1, HCDR2 and HCDR3; and/or
Three light chain variable (V L ) Domain CDR: LCDR1, LCDR2, and LCDR3; wherein the method comprises the steps of
HCDR1 comprises an amino acid sequence having at least 95% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs 1145-1191 and 2003-2009;
HCDR2 comprises an amino acid sequence having at least 95% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs 1192-1238 and 2010-2016;
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs 1239-1285 and 2017-2023;
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 1286-1332 and 2024-2030;
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1333-1379 and 2031-2037; and is also provided with
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 1380-1426 and 2038-2044.
The polypeptide of embodiment 158, which comprises a combination of HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, selected from the group consisting of:
1145, 1192, 1239, 1286, 1333, and 1380;
1146, 1193, 1240, 1287, 1334, and 1381;
1147, 1194, 1241, 1288, 1335, and 1382;
1148, 1195, 1242, 1289, 1336, and 1383;
1149, 1196, 1243, 1290, 1337 and 1384;
1150, 1197, 1244, 1291, 1338 and 1385;
1151, 1198, 1245, 1292, 1339 and 1386;
1152, 1199, 1246, 1293, 1340, and 1387;
1153, 1200, 1247, 1294, 1341 and 1388;
1154, 1201, 1248, 1295, 1342 and 1389;
1155, 1202, 1249, 1296, 1343 and 1390;
1156, 1203, 1250, 1297, 1344 and 1391;
1157, 1204, 1251, 1298, 1345 and 1392;
1158, 1205, 1252, 1299, 1346, and 1393;
1159, 1206, 1253, 1300, 1347, and 1394;
1160, 1207, 1254, 1301, 1348, and 1395;
1161, 1208, 1255, 1302, 1349, and 1396;
1162, 1209, 1256, 1303, 1350, and 1397;
1163, 1210, 1257, 1304, 1351 and 1398;
1164, 1211, 1258, 1305, 1352 and 1399;
1165, 1212, 1259, 1306, 1353 and 1400;
1166, 1213, 1260, 1307, 1354 and 1401;
1167, 1214, 1261, 1308, 1355 and 1402;
1168, 1215, 1262, 1309, 1356 and 1403;
1169, 1216, 1263, 1310, 1357 and 1404;
1170, 1217, 1264, 1311, 1358 and 1405;
1171, 1218, 1265, 1312, 1359 and 1406;
1172, 1219, 1266, 1313, 1360 and 1407;
1173, 1220, 1267, 1314, 1361 and 1408;
1174, 1221, 1268, 1315, 1362 and 1409;
1175, 1222, 1269, 1316, 1363 and 1410;
1176, 1223, 1270, 1317, 1364 and 1411;
1177, 1224, 1271, 1318, 1365 and 1412;
1178, 1225, 1272, 1319, 1366 and 1413;
1179, 1226, 1273, 1320, 1367 and 1414;
1180, 1227, 1274, 1321, 1368 and 1415;
1181, 1228, 1275, 1322, 1369 and 1416;
1182, 1229, 1276, 1323, 1370 and 1417;
1183, 1230, 1277, 1324, 1371 and 1418;
1184, 1231, 1278, 1325, 1372, and 1419;
1185, 1232, 1279, 1326, 1373 and 1420;
1186, 1233, 1280, 1327, 1374, and 1421;
1187, 1234, 1281, 1328, 1375 and 1422;
1188, 1235, 1282, 1329, 1376 and 1423;
1189, 1236, 1283, 1330, 1377, and 1424;
1190, 1237, 1284, 1331, 1378, and 1425;
1191, 1238, 1285, 1332, 1379, and 1426;
2003, 2010, 2017, 2024, 2031 and 2038;
2004, 2011, 2018, 2025, 2032, and 2039;
2005, 2012, 2019, 2026, 2033 and 2040;
2006, 2013, 2020, 2027, 2034, and 2041;
2007, 2014, 2021, 2028, 2035 and 2042;
2008, 2015, 2022, 2029, 2036, and 2043; and
2009, 2016, 2023, 2030, 2037 and 2044;
or a combination of HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3 having at least 95% sequence identity with each of the foregoing.
Example 160 the polypeptide of example 158, which comprises V H Domain and V L Domain, wherein:
the V is H The domain comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs 1427-1473 and 2045-2051; and/or
The V is L The domain comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1474-1520 and 2052-2058.
Example 161 the polypeptide of example 160 comprising V selected from H Domain and V L Combination of domains:
1427 and 1474;
1428 and 1475;
1429 and 1476;
1430 and 1477;
1431 and 1478;
1432 and 1479;
1433 and 1480;
1434 and 1481;
1435 and 1482;
1436 and 1483;
1437 and 1484;
1438 and 1485;
1439 and 1486;
1440 and 1487;
1441 and 1488;
1442 and 1489;
1443 and 1490;
1444 and 1491;
1445 and 1492;
1446 and 1493;
1447 and 1494;
1448 and 1495;
1449 and 1496;
1450 and 1497;
1451 and 1498;
1452 and 1499;
1453 and 1500;
1454 and 1501;
1455 and 1502;
1456 and 1503;
1457 and 1504;
1458 and 1505;
1459 and 1506;
1460 and 1507;
1461 and 1508;
1462 and 1509;
1463 and 1510;
1464 and 1511;
1465 and 1512;
1466 and 1513;
1467 and 1514;
1468 and 1515;
1469 and 1516;
1470 and 1517;
1471 and 1518;
1472 and 1519;
1473 and 1520;
2045 and 2052;
2046 and 2053;
2047 and 2054;
2048 and 2055;
2049 and 2056;
2050 and 2057; and
2051 and 2058;
or V having at least 95% sequence identity to the preceding H Domain and V L Combinations of domains.
Example 162. A polypeptide that binds FLT3, the polypeptide comprising:
three heavy chain variable (V H ) Domain CDR: HCDR1, HCDR2 and HCDR3; and/or
Three light chain variable (V L ) Domain CDR: LCDR1, LCDR2, and LCDR3; wherein the method comprises the steps of
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 2059-2152;
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 2153-2246;
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 2247-2340;
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 2341-2434;
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 2435-2528; and is also provided with
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 2529-2622.
Embodiment 163 the polypeptide of embodiment 162, comprising a combination of HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, selected from the group consisting of:
2059, 2153, 2247, 2341, 2435 and 2529;
2060, 2154, 2248, 2342, 2436 and 2530;
2061, 2155, 2249, 2343, 2437 and 2531;
2062, 2156, 2250, 2344, 2438 and 2532;
2063, 2157, 2251, 2345, 2439, and 2533;
2064, 2158, 2252, 2346, 2440 and 2534;
2065, 2159, 2253, 2347, 2441 and 2535;
2066, 2160, 2254, 2348, 2442 and 2536;
2067, 2161, 2255, 2349, 2443 and 2537;
2068, 2162, 2256, 2350, 2444 and 2538;
2069, 2163, 2257, 2351, 2445 and 2539;
2070, 2164, 2258, 2352, 2446 and 2540;
2071, 2165, 2259, 2353, 2447 and 2541;
2072, 2166, 2260, 2354, 2448 and 2542;
2073, 2167, 2261, 2355, 2449 and 2543;
2074, 2168, 2262, 2356, 2450 and 2544;
2075, 2169, 2263, 2357, 2451 and 2545;
2076, 2170, 2264, 2358, 2452 and 2546;
2077, 2171, 2265, 2359, 2453 and 2547;
2078, 2172, 2266, 2360, 2454 and 2548;
2079, 2173, 2267, 2361, 2455 and 2549;
2080, 2174, 2268, 2362, 2456, and 2550;
2081, 2175, 2269, 2363, 2457, and 2551;
2082, 2176, 2270, 2364, 2458, and 2552;
2083, 2177, 2271, 2365, 2459, and 2553;
2084, 2178, 2272, 2366, 2460, and 2554;
2085, 2179, 2273, 2367, 2461, and 2555;
2086, 2180, 2274, 2368, 2462, and 2556;
2087, 2181, 2275, 2369, 2463, and 2557;
2088, 2182, 2276, 2370, 2464, and 2558;
2089, 2183, 2277, 2371, 2465, and 2559;
2090, 2184, 2278, 2372, 2466 and 2560;
2091, 2185, 2279, 2373, 2467 and 2561;
2092, 2186, 2280, 2374, 2468 and 2562;
2093, 2187, 2281, 2375, 2469, and 2563;
2094, 2188, 2282, 2376, 2470 and 2564;
2095, 2189, 2283, 2377, 2471 and 2565;
2096, 2190, 2284, 2378, 2472 and 2566;
2097, 2191, 2285, 2379, 2473, and 2567;
2098, 2192, 2286, 2380, 2474 and 2568;
2099, 2193, 2287, 2381, 2475 and 2569;
2100, 2194, 2288, 2382, 2476, and 2570;
2101, 2195, 2289, 2383, 2477, and 2571;
2102, 2196, 2290, 2384, 2478 and 2572;
2103, 2197, 2291, 2385, 2479 and 2573;
2104, 2198, 2292, 2386, 2480 and 2574;
2105, 2199, 2293, 2387, 2481 and 2575;
2106, 2200, 2294, 2388, 2482 and 2576;
2107, 2201, 2295, 2389, 2483 and 2577;
2108, 2202, 2296, 2390, 2484 and 2578;
2109, 2203, 2297, 2391, 2485 and 2579;
2110, 2204, 2298, 2392, 2486 and 2580;
2111, 2205, 2299, 2393, 2487 and 2581;
2112, 2206, 2300, 2394, 2488 and 2582;
2113, 2207, 2301, 2395, 2489 and 2583;
2114, 2208, 2302, 2396, 2490 and 2584;
2115, 2209, 2303, 2397, 2491 and 2585;
2116, 2210, 2304, 2398, 2492 and 2586;
2117, 2211, 2305, 2399, 2493 and 2587;
2118, 2212, 2306, 2400, 2494 and 2588;
2119, 2213, 2307, 2401, 2495 and 2589;
2120, 2214, 2308, 2402, 2496 and 2590;
2121, 2215, 2309, 2403, 2497 and 2591;
2122, 2216, 2310, 2404, 2498 and 2592;
2123, 2217, 2311, 2405, 2499 and 2593;
2124, 2218, 2312, 2406, 2500 and 2594;
2125, 2219, 2313, 2407, 2501 and 2595;
2126, 2220, 2314, 2408, 2502 and 2596;
2127, 2221, 2315, 2409, 2503 and 2597;
2128, 2222, 2316, 2410, 2504 and 2598;
2129, 2223, 2317, 2411, 2505 and 2599;
2130, 2224, 2318, 2412, 2506 and 2600;
2131, 2225, 2319, 2413, 2507 and 2601;
2132, 2226, 2320, 2414, 2508 and 2602;
2133, 2227, 2321, 2415, 2509 and 2603;
2134, 2228, 2322, 2416, 2510 and 2604;
2135, 2229, 2323, 2417, 2511 and 2605;
2136, 2230, 2324, 2418, 2512, and 2606;
2137, 2231, 2325, 2419, 2513, and 2607;
2138, 2232, 2326, 2420, 2514 and 2608;
2139, 2233, 2327, 2421, 2515 and 2609;
2140, 2234, 2328, 2422, 2516, and 2610;
2141, 2235, 2329, 2423, 2517, and 2611;
2142, 2236, 2330, 2424, 2518, and 2612;
2143, 2237, 2331, 2425, 2519 and 2613;
2144, 2238, 2332, 2426, 2520 and 2614;
2145, 2239, 2333, 2427, 2521, and 2615;
2146, 2240, 2334, 2428, 2522 and 2616;
2147, 2241, 2335, 2429, 2523 and 2617;
2148, 2242, 2336, 2430, 2524, and 2618;
2149, 2243, 2337, 2431, 2525, and 2619;
2150, 2244, 2338, 2432, 2526 and 2620;
2151, 2245, 2339, 2433, 2527 and 2621; and
2152, 2246, 2340, 2434, 2528 and 2622;
or a combination of HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3 having at least 95% sequence identity with each of the foregoing.
Example 164 the polypeptide of example 162 comprising V H Domain and V L Domain, wherein:
the V is H The domain comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs 2623-2716; and/or
The V is L The domain comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 2717-2810.
Example 165 the polypeptide of example 164, which comprises V selected from H Domain and V L Combination of domains:
SEQ ID NOS 2623 and 2717;
SEQ ID NOS 2624 and 2718;
SEQ ID NOS 2625 and 2719;
2626 and 2720;
2627 and 2721;
2628 and 2722;
SEQ ID NOS 2629 and 2723;
2630 and 2724;
2631 and 2725;
2632 and 2726;
2633 and 2727;
2634 and 2728;
2635 and 2729;
2636 and 2730;
2637 and 2731;
2638 and 2732;
2639 and 2733;
2640 and 2734;
2641 and 2735;
2642 and 2736;
2643 and 2737;
2644 and 2738;
2645 and 2739;
2646 and 2740;
2647 and 2741;
2648 and 2742;
2649 and 2743;
2650 and 2744;
2651 and 2745;
2652 and 2746;
2653 and 2747;
2654 and 2748;
2655 and 2749;
2656 and 2750;
2657 and 2751;
2658 and 2752;
2659 and 2753;
2660 and 2754;
2661 and 2755;
2662 and 2756;
2663 and 2757;
2664 and 2758;
2665 and 2759;
2666 and 2760;
2667 and 2761;
2668 and 2762;
2669 and 2763;
2670 and 2764;
2671 and 2765;
2672 and 2766;
2673 and 2767;
2674 and 2768;
2675 and 2769;
2676 and 2770;
2677 and 2771;
2678 and 2772;
2679 and 2773;
2680 and 2774;
2681 and 2775;
2682 and 2776;
2683 and 2777;
2684 and 2778;
2685 and 2779;
2686 and 2780;
2687 and 2781;
2688 and 2782;
2689 and 2783;
2690 and 2784;
2691 and 2785;
2692 and 2786;
2693 and 2787;
2694 and 2788;
2695 and 2789;
2696 and 2790;
2697 and 2791;
2698 and 2792;
2699 and 2793;
2700 and 2794;
2701 and 2795;
2702 and 2796;
2703 and 2797;
2704 and 2798;
2705 and 2799;
2706 and 2800;
2707 and 2801;
2708 and 2802;
2709 and 2803;
2710 and 2804;
2711 and 2805;
2712 and 2806;
2713 and 2807;
2714 and 2808;
2715 and 2809; and
2716 and 2810;
or V having at least 95% sequence identity to the preceding H Domain and V L Combinations of domains.
Embodiment 165 the polypeptide of any of embodiments 154-164, wherein
The HCDR1, HCDR2 and HCDR3 and/or the LCDR1, LCDR2 and LCDR3, or
V is the same as H Domain and/or V L Domain
Has at least 97%, 98% or 99% sequence identity to said amino acid sequence.
Example 166. A single chain variable fragment (scFv) comprising the polypeptide of any one of examples 154-164.
Example 167 a monoclonal antibody (mAb) or antigen-binding fragment thereof comprising the polypeptide of any one of examples 154-164.
Example 168. The mAb of example 167 or antigen-binding fragment thereof, wherein the mAb is of an IgG, igM, or IgA isotype.
Example 169. The mAb of example 170, or an antigen-binding fragment thereof, wherein the mAb is of the IgG1 isotype.
Example 170 the mAb of example 170, or an antigen-binding fragment thereof, wherein the mAb is of the IgG3 isotype.
Example 171 the mAb of example 170, or antigen-binding fragment thereof, wherein the mAb is of the IgG4 isotype.
Example 172 the mAb or antigen-binding fragment thereof of example 170, wherein the mAb is human or humanized.
Embodiment 173 an antibody-drug conjugate (ADC) comprising the mAb or antigen-binding fragment thereof of any one of embodiments 167-172.
Embodiment 174 the ADC of embodiment 173 having formula I:
Ab-(L-D) p
(I)
wherein:
ab is an antibody comprising the polypeptide of any one of embodiments 1-43, or the antibody of any one of embodiments 45-51, or an antigen-binding fragment of either of the foregoing;
l is a linker;
d is a drug; and is also provided with
p is from about 1 to about 20.
Embodiment 175 the ADC of embodiment 174, wherein D is selected from saporin, MMAE, MMAF, DM1, and DM4.
Embodiment 176 a Chimeric Antigen Receptor (CAR) comprising an extracellular ligand binding domain comprising the polypeptide of any one of embodiments 1-69.
Embodiment 177 the CAR of embodiment 176, further comprising:
a hinge domain;
a transmembrane domain;
optionally, one or more co-stimulatory domains; and
cytoplasmic signaling domains.
Embodiment 178 the CAR of embodiment 177, wherein the hinge domain is selected from fceriia, CD8 a, CD28, and IgG1.
Embodiment 179 the CAR of embodiment 178, wherein the hinge domain is CD8 a.
Embodiment 180 the CAR of any one of embodiments 177-179, wherein the transmembrane domain is selected from the group consisting of the alpha, beta, or zeta chain of the T cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD9, CD16, CD22, CD33, CD37, CD64, CDs0, CD86, CD134, CD137, and CD154.
Embodiment 181. The CAR of embodiment 180, wherein the transmembrane domain is CD28.
Embodiment 182 the CAR of any one of embodiments 177-181, wherein the cytoplasmic signaling domain is selected from the group consisting of CD8, cd3ζ, cd3δ, cd3γ, cd3ε, CD22, CD32, DAP10, DAP12, CD66d, CD79a, CD79b, fcyriγ, fcrγ, fcrβ, and fcrepsilon.
Example 183 the CAR of example 182, wherein the cytoplasmic signaling domain is CD3 zeta.
Embodiment 184. The CAR of any one of embodiments 177-183, wherein one co-stimulatory domain is selected from the group consisting of 4-1BB, CD28 and ICOS.
Embodiment 185 the CAR of embodiment 184, wherein the co-stimulatory domain is CD28.
Embodiment 186 the CAR of embodiment 184, wherein the co-stimulatory domain is 4-1BB.
Example 187 the CAR of example 184, comprising two or more co-stimulatory domains.
Example 188. The CAR of example 184, wherein two of the co-stimulatory domains are CD28 and 4-1BB.
Embodiment 189 a nucleotide sequence encoding the polypeptide, scFv, mAb or CAR of any one of embodiments 154-188.
Example 190. A vector comprising the nucleotide sequence set forth in example 189.
Embodiment 191. The vector of embodiment 190, wherein the vector is a lentiviral vector.
Embodiment 192 the vector of embodiment 191 wherein the lentiviral vector comprises a VSVG domain.
Example 193 an engineered immune effector cell that expresses the CAR of any one of examples 176-188 on the surface of the cell.
Example 194. The engineered immune effector cell of example 193, wherein the engineered immune effector cell expresses on the surface of the cell:
a first polymorphic variant of a human cancer cell antigen; and
a CAR that is selective for a second polymorphic variant relative to a first polymorphic variant of the antigen.
Example 195. The engineered immune effector cell of example 193, wherein the cell is a primary cell.
Example 196. The engineered immune effector cell of example 193, wherein the cell is derived from:
induced pluripotent stem cells (ipscs);
cord blood;
peripheral blood; or alternatively
Immortalized cell lines.
Example 197 the engineered immune effector cell of example 196, wherein the immortalized cell line is NK-92.
Embodiment 198 the engineered immune cell of any one of embodiments 193-197, wherein the cell is selected from the group consisting of a T cell, a Natural Killer (NK) cell, a constant natural killer T (iNKT) cell, a macrophage, and a dendritic cell.
Example 199. The engineered immune effector cell of example 198, wherein the cell is a T cell.
Example 200. The engineered immune effector cell of example 199, wherein the T cell is selected from an inflammatory T-lymphocyte, a cytotoxic T-lymphocyte, a regulatory T-lymphocyte, or a helper T-lymphocyte.
Example 201. The engineered immune effector cell of example 199, wherein the engineered immune effector cell lacks subunits of the T cell receptor complex.
Example 202. The engineered immune effector cell of example 201, wherein the subunit of the T cell receptor complex is selected from the group consisting of Tcra (TRAC), tcrp, tcrδ, tcrγ, cd3ε, cd3γ, cd3δ, and cd3ζ.
Embodiment 203 the engineered immune effector cell of any of embodiments 193-202, wherein the engineered immune effector cell lacks a cell surface protein that is a target of the CAR.
Embodiment 204. The engineered immune effector cell of embodiment 198, wherein the engineered immune effector cell is an NK cell.
Embodiment 205. The engineered immune effector cell of embodiment 204, wherein the engineered immune effector cell is a memory-like (ML) NK cell.
Embodiment 206. The engineered immune effector cell of embodiment 205, wherein the engineered immune effector cell is a cytokine-induced memory-like (CIML) NK cell.
Example 207. The engineered immune effector cell of example 198, wherein the engineered immune effector cell is an iNKT cell.
Example 208. A method of treating cancer in a patient, the method comprising administering to the cancer patient a therapeutically effective amount of:
the monoclonal antibody (mAb) or antigen-binding fragment thereof of any one of embodiments 167-170;
the antibody-drug conjugate (ADC) of any one of embodiments 173-175; or alternatively
The engineered immune effector cell of any one of embodiments 193-207.
Embodiment 209 the method of embodiment 208, wherein the cancer is a hematological malignancy.
Embodiment 210 the method of embodiment 209, wherein the hematological malignancy is multiple myeloma.
Embodiment 211 the method of embodiment 210, wherein the hematological malignancy is Acute Myeloid Leukemia (AML).
Polypeptides
Polypeptides, such as monoclonal antibodies (mabs) and functional fragments thereof, synthetic antigen binding proteins, such as single chain variable fragments (scFv), and Chimeric Antigen Receptors (CARs), that can specifically recognize tumor-associated antigens (TAAs) on cancer cells, such as those expressing CD33, FLT3, and CLL-1. In some embodiments, the mAb, scFv, or CAR recognizes polymorphic variants of CD33, FLT3, and CLL-1 expressed on cancer cells; in some embodiments, they are selective for one polymorphic variant over other polymorphic variants. Immune effector cells, such as T cells, natural Killer (NK) cells, and constant natural killer T (iNKT) cells, engineered to express CARs that specifically recognize tumor-associated antigens (TAA) CD33, FLT3, and CLL-1 or polymorphic variants of CD33, FLT3, and CLL-1 are also disclosed. Also disclosed are methods of providing anti-tumor immunity in a subject having a CD33, FLT3, and CLL-1 expressing cancer using the disclosed monoclonal antibodies and CAR-expressing immune effector cells.
Antibodies that can be used in the disclosed compositions and methods include any class of whole immunoglobulins (i.e., intact antibodies), fragments thereof, and (where the term is used more loosely) synthetic proteins (e.g., single chain variable fragments (scFv)) that contain at least the antigen-binding variable domain of the antibody. The variable domains vary in sequence among the various antibodies and are used for binding and specificity of each particular antibody for its particular antigen. However, variability is not typically evenly distributed over the variable domains of antibodies. It is typically concentrated in three segments called Complementarity Determining Regions (CDRs) or hypervariable regions in both the light chain variable domain and the heavy chain variable domain. The more highly conserved portions of the variable domains are called the Framework (FR). The variable domains of the natural heavy and light chains each comprise four FR regions connected by three CDRs, which mainly adopt a β -sheet configuration, which CDRs form loops connecting the β -sheet structure and in some cases form part of the β -sheet structure. The CDRs in each chain are joined together very close together by the FR regions and together with the CDRs from the other chain promote the formation of the antigen binding site of the antibody.
Transgenic animals (e.g., mice) that are capable of producing a complete set of human antibodies after immunization without endogenous immunoglobulin production can be used. For example, it has been described that homozygous deletion of the antibody heavy chain junction (J (H)) gene in chimeric and germline mutant mice results in complete inhibition of endogenous antibody production. Transfer of an array of human germline immunoglobulin genes into such germline mutant mice will result in the production of human antibodies upon antigen challenge. Human antibodies can also be generated in phage display libraries. The techniques of Cote et al and Boerner et al may also be used to prepare human monoclonal antibodies.
Optionally, the antibodies are produced in other species and "humanized" for administration in humans. Humanized forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (e.g., fv, fab, fab ', F (ab') 2 or other antigen binding subsequences of antibodies) containing minimal sequence derived from non-human immunoglobulins. Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a Complementarity Determining Region (CDR) of the recipient antibody are replaced by residues from a CDR of a non-human species (e.g., mouse, rat or rabbit) (donor antibody) having the desired specificity, affinity and capacity. In some cases, fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues found in neither the recipient antibody nor the imported CDR or framework sequences. Generally, a humanized antibody will comprise substantially all of at least one (typically two) variable domain, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. Optimally, the humanized antibody will also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
Methods for humanizing non-human antibodies are well known in the art. Typically, humanized antibodies have one or more amino acid residues introduced therein from a non-human source. These non-human amino acid residues are often referred to as "import" residues, which are typically taken from an "import" variable domain. Antibody humanization techniques typically involve the use of recombinant DNA techniques to manipulate DNA sequences encoding one or more polypeptide chains of an antibody molecule. Humanization can be essentially performed by substituting rodent CDR or CDR sequences for the corresponding sequences of human antibodies according to the method of Winter and co-workers (Jones et al, nature, 321:522-525 (1986); riechmann et al, nature, 332:323-327 (1988); verhoeyen et al, science, 239:1534-1536 (1988)). Thus, humanized versions of non-human antibodies (or antigen binding fragments thereof) are chimeric antibodies or fragments (U.S. Pat. No. 4,816,567) in which substantially less than the complete human variable domain is replaced with a corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues, and possibly some FR residues, are replaced with residues from similar sites in rodent antibodies.
Embodiments of the present disclosure include polypeptides, particularly monoclonal antibodies (mabs), antigen-binding fragments thereof, as defined by reference to structural featuresSynthetic antigen binding proteins (such as scFv) and Chimeric Antigen Receptors (CARs), which are structural features, namely Complementarity Determining Regions (CDRs), heavy or light chain variable domains (V H Or V L ) Or a specific amino acid sequence of a full-length heavy or light chain (HC or LC). The monoclonal antibodies of the disclosure, or antigen binding fragments thereof, bind, for example, CD33, FLT3, or CLL-1, or polymorphic variants thereof.
Antibody fragments having biological activity are also disclosed. Whether attached to other sequences or not, these fragments include insertions, deletions, substitutions or other selected modifications of specific regions or specific amino acid residues, provided that the activity of the fragment is not significantly altered or compromised compared to the unmodified antibody or antibody fragment.
The techniques may also be applied to the production of synthetic single chain antibodies (in fact, antibody-like fusion proteins) specific for the antigen proteins of the present disclosure. Methods for producing single chain antibodies are well known to those skilled in the art. Single chain antibodies can be produced by fusing the variable domains of the heavy and light chains together using a short peptide linker, thereby reconstructing the antigen binding site on a single molecule. Single chain antibody variable fragments (scFvs) have been developed in which the C-terminus of one variable domain is linked to the N-terminus of another variable domain via a 15 to 25 amino acid peptide or linker without significantly disrupting antigen binding or specificity of binding. The linker is selected to allow the heavy and light chains to be joined together in their proper conformational orientation.
The monoclonal antibodies of the present disclosure, or antigen binding fragments thereof, comprise at least one, typically at least three CDR sequences, either in combination with framework sequences from human variable regions or in the form of isolated CDR peptides. In some embodiments, an antibody comprises at least one heavy chain comprising three heavy chain CDR sequences in a variable region framework, which may be a human or murine variable region framework, and at least one light chain comprising three light chain CDR sequences in a variable region framework, which may be a murine or human variable region framework, provided herein.
anti-CD 33 polypeptides
In some embodiments of the disclosure, anti-CD 33 polypeptides, including mabs, antigen-binding fragments thereof, and synthetic fusion proteins, such as single chain variable fragments (scFv), are provided, which anti-CD 33 polypeptides comprise one or more Complementarity Determining Regions (CDRs) that recognize and bind CD 33. In some embodiments, anti-CD 33 polypeptides include mabs, antigen-binding fragments thereof, and synthetic fusion proteins (e.g., single chain variable fragments (scFv)), which anti-CD 33 polypeptides selectively bind to a first polymorphic variant of CD33 relative to a second polymorphic variant of CD 33; or a second polymorphic variant that selectively binds CD33 relative to the first polymorphic variant. In some embodiments, the binding has a selectivity of at least 2-fold, 10-fold, or 30-fold.
In some embodiments, the first polymorphic variant of CD33 is R69 and the second polymorphic variant of CD33 is G69; or the first polymorphic variant of CD33 is G69 and the second polymorphic variant of CD33 is R69.
In some embodiments of the disclosure, anti-CD 33 polypeptides, including mabs, antigen-binding fragments thereof, and synthetic fusion proteins, such as single chain variable fragments (scFv), are provided, which anti-CD 33 polypeptides comprise one or more Complementarity Determining Regions (CDRs) that recognize and bind CD 33. The CDRs and V for the anti-CD 33 polypeptides described herein for binding CD33 are provided in the tables and examples below H And V L Domain sequence.
Thus, provided herein are heavy chain variable (V H ) Domain CDR1 (HCDR 1), V H Domains CDR2 (HCDR 2) and V H Domain CDR3 (HCDR 3), wherein the HCDR1 comprises an amino acid sequence selected from any one of SEQ ID NOs 1-25 and 201-217; HCDR2 comprises an amino acid sequence selected from any one of SEQ ID NOs 26-50 and 218-234; and HCDR3 comprises an amino acid sequence selected from any one of SEQ ID NOs 51-75 and 235-251. Also provided are HCDR1, HCDR2 and HCDR3, and polypeptides comprising the same, wherein the HCDR1 comprises an amino acid sequence selected from any one of SEQ ID NOs 1 to 25; HCDR2 comprises an amino acid sequence selected from any one of SEQ ID NOs 26 to 50; and HCDR3 comprises an amino acid sequence selected from any one of SEQ ID NOs 51-75. Also provided are HCDR1, HCDR2 and HCDR 3, and polypeptides comprising them, wherein the HCDR1 comprises an amino acid sequence selected from any one of SEQ ID NOs 201-217; HCDR2 comprises an amino acid sequence selected from any one of SEQ ID NOs 218 to 234; and HCDR3 comprises an amino acid sequence selected from any one of SEQ ID NOs 235-251.
V comprising one or more of these CDRs is also provided H A domain. V of anti-CD 33 mAb or antigen binding fragment thereof H The domains may comprise a combination of any of the listed HCDR1 sequences with any of the HCDR2 sequences, and with any of the HCDR3 sequences. However, in certain embodiments, the HCDR1, HCDR2 and HCDR3 sequences provided are derived from a single common V H Domains, examples of which are described herein.
The anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding proteins (e.g., scFv) may additionally comprise a light chain variable (V L ) Domain of V L Domain and V H The domains mate to form the CD33 antigen binding domain.
Thus, provided herein are light chain variable (V L ) Domain CDR1 (LCDR 1), V L Domains CDR2 (LCDR 2) and V L Domain CDR3 (LCDR 3), wherein the LCDR1 comprises an amino acid sequence selected from the group consisting of SEQ ID NOs 76-100 and 252-268; LCDR2 comprises an amino acid sequence selected from SEQ ID NOS 101-125 and 269-285; and LCDR3 comprises an amino acid sequence selected from SEQ ID NOS 126-150 and 286-302. Also provided are LCDR1, LCDR2 and LCDR3, and polypeptides comprising the same, wherein the LCDR1 comprises an amino acid sequence selected from any one of SEQ ID NOs 76-100; LCDR2 comprises an amino acid sequence selected from any one of SEQ ID NOs 101-125; and LCDR3 comprises an amino acid sequence selected from any one of SEQ ID NOS 125-150. Also provided are LCDR1, LCDR2 and LCDR3, and polypeptides comprising the same, wherein LCDR1 comprises an amino acid sequence selected from any one of SEQ ID NOs 252-268; LCDR2 comprises an amino acid sequence selected from any one of SEQ ID NOS 269-285; and LCDR3 comprises an amino acid sequence selected from any one of SEQ ID NOS 286-302.
V comprising one or more of these CDRs is also provided L A domain. V of anti-CD 33 mAb, antigen-binding fragment thereof, or synthetic antigen-binding protein (e.g., scFv) L The domains may comprise a combination of any of the listed LCDR1 sequences with any of the LCDR2 sequences, and with any of the LCDR3 sequences. However, in certain embodiments, the LCDR1, LCDR2, and LCDR3 sequences are derived from a single common V L Domains, examples of which are described herein.
Also provided are mabs, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv) comprising the CDRs, V disclosed herein H Domain and/or V L A domain. Comprises and V L V of domain pairing H Any given anti-CD 33 mAb (and certain antigen-binding fragments thereof) or scFv of a domain will comprise a combination of the following six (6) CDRs: v (V) H Domain CDR1 (HCDR 1), V H Domains CDR2 (HCDR 2) and V H Domain CDR3 (HCDR 3), V L Domain CDR1 (LCDR 1), V L Domains CDR2 (LCDR 2) and V L Domain CDR3 (LCDR 3). Although all combinations of six (6) CDRs selected from the above CDR amino acid sequences are permissible and within the scope of the present disclosure, certain combinations of six (6) CDRs are provided herein.
In some embodiments, the combination of six (6) CDRs is selected from the combinations described in each of polypeptide numbers 1-42. In some embodiments, the combination of six (6) CDRs is selected from the combinations described in each of polypeptide numbers 1-25. In some embodiments, the combination of six (6) CDRs is selected from the combinations described in each of polypeptide numbers 26-42.
In some embodiments, the anti-CD 33 mAb, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv) comprise a V selected from any of SEQ ID NO 151-175 and 303-319 H Domain of V H The domain has an amino acid sequence that exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to one of the amino acid sequences. In some embodiments, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprise V selected from any of SEQ ID NOs 151-175 H Domain of V H The domain has an amino acid sequence that exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to one of the amino acid sequences. In some embodiments, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprises V selected from any one of SEQ ID NOs 303-319 H Domain of V H The domain has an amino acid sequence that exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to one of the amino acid sequences.
Alternatively or additionally, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprise V having an amino acid sequence selected from any one of SEQ ID NOs 176-200 and 320-336 L A domain, and the amino acid sequence exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity with one of the amino acid sequences. In some embodiments, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprise V having an amino acid sequence selected from any one of SEQ ID NOs 176-200 L A domain, and the amino acid sequence exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity with one of the amino acid sequences. In some embodiments, the anti-CD 33 mAb, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv) comprise a V having an amino acid sequence selected from any one of SEQ ID NOs 320-336 L A domain, and the amino acid sequence exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity with one of the amino acid sequences.
Although selected from V listed above H Domain and V L V of the Domain amino acid sequence H Domain and V L All possible pairings of domains are permissible and within the scope of the present disclosure, but some embodiments still provide V H Domain and V L Certain combinations of domains. Thus, in some embodiments, anti-CD33 mAbs, antigen binding fragments thereof, and synthetic antigen binding proteins (e.g., scFv) comprise V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 1-42, e.g.:
151 and 176;
152 and 177;
153 and 178;
154 and 179;
155 and 180;
156 and 181;
157 and 182;
158 and 183;
159 and 184;
160 and 185;
161 and 186;
162 and 187;
163 and 188;
164 and 189;
165 and 190;
166 and 191;
167 and 192;
168 and 193;
169 and 194;
170 and 195;
171 and 196;
172 and 197;
173 and 198;
174 and 199;
175 and 200;
SEQ ID NO 303 and SEQ ID NO 320;
304 and 321;
SEQ ID NO. 305 and SEQ ID NO. 322;
306 and 323;
307 and 324;
308 and 325;
309 and 326;
310 and 327;
311 and 328;
312 and 329;
313 and 330;
314 and 331;
315 and 332;
316 and 333;
317 and 334;
318 and 335;
and
319 and 336.
In some embodiments, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprise V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 1-25, e.g.:
151 and 176;
152 and 177;
153 and 178;
154 and 179;
155 and 180;
156 and 181;
157 and 182;
158 and 183;
159 and 184;
160 and 185;
161 and 186;
162 and 187;
163 and 188;
164 and 189;
165 and 190;
166 and 191;
167 and 192;
168 and 193;
169 and 194;
170 and 195;
171 and 196;
172 and 197;
173 and 198;
174 and 199;
and
175 and 200.
In some embodiments, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprise V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 26-42, e.g.:
SEQ ID NO 303 and SEQ ID NO 320;
304 and 321;
SEQ ID NO. 305 and SEQ ID NO. 322;
306 and 323;
307 and 324;
308 and 325;
309 and 326;
310 and 327;
311 and 328;
312 and 329;
313 and 330;
314 and 331;
315 and 332;
316 and 333;
317 and 334;
318 and 335;
and
319 and 336.
In some embodiments, the anti-CD 33 antibodies, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv) may also comprise a combination of a variable heavy domain and a variable light domain, wherein the variable heavy domain comprises a V having at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to a variable heavy chain amino acid sequence as set forth above H A sequence, and/or wherein the variable light domain comprises a V having at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to a variable light domain amino acid sequence set forth above L Sequence. Can reserve the above specific V H And V L Pairing or combining for having V H And V L Domain sequences of anti-CD 33 antibodies, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv), these V H And V L Domain sequences have a specific percentage of amino acid sequence identity to these reference sequences disclosed herein.
For all embodiments in which the variable heavy and/or light chain domains of antibodies, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scfvs) are defined by a specific percentage of amino acid sequence identity to a reference sequence, V H And/or V L The domains may retain CDR sequences identical to those present in the reference sequence such that the changes exist only within the framework regions.
anti-FLT 3 polypeptides
In some embodiments of the disclosure, anti-FLT 3 polypeptides, including mabs, antigen-binding fragments thereof, and synthetic fusion proteins, such as single chain variable fragments (scFv), are provided, which comprise one or more Complementarity Determining Regions (CDRs) that recognize and bind FLT 3. In some embodiments, anti-FLT 3 polypeptides include mabs, antigen-binding fragments thereof, and synthetic fusion proteins (e.g., single-chain variable fragments (scFv)), which anti-FLT 3 polypeptides selectively bind to a first polymorphic variant of FLT3 relative to a second polymorphic variant of FLT 3; or a second polymorphic variant that selectively binds FLT3 relative to the first polymorphic variant. In some embodiments, the binding has a selectivity of at least 2-fold, 10-fold, or 30-fold.
In some embodiments, the first polymorphic variant of FLT3 is T227 and the second polymorphic variant of FLT3 is M227; or the first polymorphic variant of FLT3 is M227 and the second polymorphic variant of FLT3 is T227.
Thus, provided herein are heavy chain variable (V H ) Domain CDR1 (HCDR 1), V H Domains CDR2 (HCDR 2) and V H Domain CDR3 (HCDR 3) and polypeptides comprising the same.
V comprising one or more of these CDRs is also provided H A domain. V of anti-FLT 3 mAb, antigen binding fragment thereof, or synthetic antigen binding protein (e.g., scFv) H The domains may comprise a combination of any of the listed HCDR1 sequences with any of the HCDR2 sequences, and with any of the HCDR3 sequences. However, in certain embodiments, the HCDR1, HCDR2 and HCDR3 sequences provided are derived from a single common V H Domains, examples of which are described herein.
anti-FLT 3 mabs, antigen binding fragments thereof, and synthetic antigen binding proteins (e.g., scFv) may additionally comprise a light chain variable (V L ) Domain of V L Domain and V H The domains mate to form the FLT3 antigen binding domain.
Thus, provided herein are light chain variable (V L ) Domain CDR1 (LCDR 1), V L Domains CDR2 (LCDR 2) and V L Domain CDR3 (LCDR 3) and polypeptides comprising the same
V comprising one or more of these CDRs is also provided L A domain. V of anti-FLT 3 mAb, antigen binding fragment thereof, or synthetic antigen binding protein (e.g., scFv) L The domains may comprise a combination of any of the listed LCDR1 sequences with any of the LCDR2 sequences, and with any of the LCDR3 sequences. However, in certain embodiments, the LCDR1, LCDR2, and LCDR3 sequences are derived from a single common V L Domains, examples of which are described herein.
Also provided are mabs, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv) comprising the CDRs, V disclosed herein H Domain and/or V L A domain. Comprises and V L V of domain pairing H Any given anti-FLT 3 mAb (and certain antigen binding fragments thereof) or scFv of a domain will comprise a combination of the following six (6) CDRs: v (V) H Domain CDR1 (HCDR 1), V H Domains CDR2 (HCDR 2) and V H Domain CDR3 (HCDR 3), V L Domain CDR1 (LCDR 1), V L Domains CDR2 (LCDR 2) and V L Domain CDR3 (LCDR 3). Although all combinations of six (6) CDRs selected from the above CDR amino acid sequences are permissible and within the scope of the present disclosure, certain combinations of six (6) CDRs are provided herein.
Although selected from V listed above H Domain and V L V of the Domain amino acid sequence H Domain and V L All possible pairings of domains are permissible and within the scope of the present disclosure, but some embodiments still provide V H Domain and V L Certain combinations of domains.
In some embodiments, the anti-FLT 3 antibodies, antigen binding fragments thereof, and synthetic antigen binding proteins (e.g., scFv) may also comprise a combination of a variable heavy chain domain and a variable light chain domain, wherein the variable heavy chain domain comprises V having at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to a variable heavy chain amino acid sequence as set forth above H A sequence, and/or wherein the variable light domain comprises a V having at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to a variable light domain amino acid sequence set forth above L Sequence. Specific V which may remain in the whole part (i) H And V L Pairing or combining is used to have V with a specific percentage of amino acid sequence identity to these reference sequences disclosed herein H And V L anti-FLT 3 antibodies to domain sequences.
For antibodies therein, antigen binding thereof Fragments, and variable heavy and/or light chain domains of synthetic antigen binding proteins (e.g., scfvs) are defined by a percentage of identity to a particular amino acid sequence of a reference sequence, V H And/or V L The domains may retain CDR sequences identical to those present in the reference sequence such that the changes exist only within the framework regions.
anti-CLL-1 polypeptides
In some embodiments of the present disclosure, anti-CLL-1 polypeptides, including mabs, antigen-binding fragments thereof, and synthetic fusion proteins, such as single chain variable fragments (scFv), are provided, which comprise one or more Complementarity Determining Regions (CDRs) that recognize and bind CLL-1. In some embodiments, anti-CLL-1 polypeptides include mabs, antigen-binding fragments thereof, and synthetic fusion proteins (e.g., single chain variable fragments (scFv)), which selectively bind to a first polymorphic variant of CLL-1 relative to a second polymorphic variant of CLL-1; or a second polymorphic variant that selectively binds CLL-1 relative to the first polymorphic variant. In some embodiments, the binding has a selectivity of at least 2-fold, 10-fold, or 30-fold.
In some embodiments, the first polymorphic variant of CLL-1 is K224 and the second polymorphic variant of CLL-1 is Q244; or the first polymorphic variant of CLL-1 is Q224 and the second polymorphic variant of CLL-1 is K244.
In some embodiments of the present disclosure, anti-CLL-1 polypeptides, including mabs, antigen-binding fragments thereof, and synthetic fusion proteins, such as single chain variable fragments (scFv), are provided, which comprise one or more Complementarity Determining Regions (CDRs) that recognize and bind CLL-1. The CDRs and V for the anti-CD 33 polypeptides described herein for binding CLL-1 are provided in the tables and examples below H And V L Domain sequence.
Thus, provided herein are heavy chain variable (V H ) Domain CDR1 (HCDR 1), V H Domains CDR2 (HCDR 2) and V H Domain CDR3 (HCDR 3), wherein the HCDR1 comprises an amino acid sequence selected from any one of SEQ ID NOs 337-360 and 529-550; HCDR2 comprises a sequence selected from SEQ ID NO 361-384 and 551-572; and HCDR3 comprises an amino acid sequence selected from any one of SEQ ID NOs 385-408 and 573-594. Also provided are HCDR1, HCDR2 and HCDR3, and polypeptides comprising the same, wherein the HCDR1 comprises an amino acid sequence selected from any one of SEQ ID NOs 337 to 360; HCDR2 comprises an amino acid sequence selected from any one of SEQ ID NOs 361-384; and HCDR3 comprises an amino acid sequence selected from any one of SEQ ID NOs 361-384. Also provided are HCDR1, HCDR2 and HCDR3, and polypeptides comprising the same, wherein the HCDR1 comprises an amino acid sequence selected from any one of SEQ ID NOs 529 to 550; HCDR2 comprises an amino acid sequence selected from any one of SEQ ID NOs 551-572; and HCDR3 comprises an amino acid sequence selected from any one of SEQ ID NOs 573-594.
V comprising one or more of these CDRs is also provided H A domain. V of anti-CLL-1 mAb, antigen-binding fragment thereof, or synthetic antigen-binding protein (e.g., scFv) H The domains may comprise a combination of any of the listed HCDR1 sequences with any of the HCDR2 sequences, and with any of the HCDR3 sequences. However, in certain embodiments, the HCDR1, HCDR2 and HCDR3 sequences provided are derived from a single common V H Domains, examples of which are described herein.
anti-CLL-1 mabs, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv) may additionally comprise a light chain variable (V L ) Domain of V L Domain and V H The domains mate to form the CLL-1 antigen binding domain.
Thus, provided herein are light chain variable (V L ) Domain CDR1 (LCDR 1), V L Domains CDR2 (LCDR 2) and V L Domain CDR3 (LCDR 3), and polypeptides comprising the same, wherein the LCDR1 comprises an amino acid sequence selected from the group consisting of SEQ ID NOs 409-432 and 595-616; LCDR2 comprises an amino acid sequence selected from SEQ ID NOS 433-456 and 617-638; and LCDR3 comprises an amino acid sequence selected from SEQ ID NOS 457-480 and 639-660. Also provided are LCDR1, LCDR2 and LCDR3, and polypeptides comprising the same, wherein the LCDR1 comprises an amino acid sequence selected from any one of SEQ ID NOs 409-432; LCDR2 comprises a sequence selected from SEQ ID NOS 433-456 The amino acid sequence of any one of the above; and LCDR3 comprises an amino acid sequence selected from any one of SEQ ID NOS 433-456. Also provided are LCDR1, LCDR2 and LCDR3, and polypeptides comprising the same, wherein the LCDR1 comprises an amino acid sequence selected from any one of SEQ ID NOs 595-616; LCDR2 comprises an amino acid sequence selected from any one of SEQ ID NOs 617-638; and LCDR3 comprises an amino acid sequence selected from any one of SEQ ID NOs 639-660.
V comprising one or more of these CDRs is also provided L A domain. V of anti-CLL-1 mAb, antigen-binding fragment thereof, or synthetic antigen-binding protein (e.g., scFv) L The domains may comprise a combination of any of the listed LCDR1 sequences with any of the LCDR2 sequences, and with any of the LCDR3 sequences. However, in certain embodiments, the LCDR1, LCDR2, and LCDR3 sequences are derived from a single common V L Domains, examples of which are described herein.
Also provided are mabs, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv) comprising the CDRs, V disclosed herein H Domain and/or V L A domain. Comprises and V L V of domain pairing H Any given anti-CLL-1 mAb (and certain antigen-binding fragments thereof) or scFv of a domain will comprise a combination of the following six (6) CDRs: v (V) H Domain CDR1 (HCDR 1), V H Domains CDR2 (HCDR 2) and V H Domain CDR3 (HCDR 3), V L Domain CDR1 (LCDR 1), V L Domains CDR2 (LCDR 2) and V L Domain CDR3 (LCDR 3). Although all combinations of six (6) CDRs selected from the above CDR amino acid sequences are permissible and within the scope of the present disclosure, certain combinations of six (6) CDRs are provided herein.
In some embodiments, the combination of six (6) CDRs is selected from the combinations described in each of polypeptide numbers 43-88. In some embodiments, the combination of six (6) CDRs is selected from the combinations described in each of polypeptide numbers 43-66. In some embodiments, the combination of six (6) CDRs is selected from the combinations described in each of polypeptide numbers 67-88.
In some embodiments, anti-CLL-1 mAb. The antigen binding fragment thereof, and the synthetic antigen binding protein (e.g., scFv) comprises V selected from any one of SEQ ID NOs 481-504 and 661-682 H Domain of V H The domain has an amino acid sequence that exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to one of the amino acid sequences. In some embodiments, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprises V selected from any one of SEQ ID NOs 481-504 H Domain of V H The domain has an amino acid sequence that exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to one of the amino acid sequences. In some embodiments, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprise V selected from any one of SEQ ID NOs 661-682 H Domain of V H The domain has an amino acid sequence that exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to one of the amino acid sequences.
Alternatively or additionally, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprise V having an amino acid sequence selected from any one of SEQ ID NOs 505-528 and 683-704 L A domain, and the amino acid sequence exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity with one of the amino acid sequences. In some embodiments, the anti-CD 33 mAb, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv) comprise a V having an amino acid sequence selected from any one of SEQ ID NOs 505-528 L A domain, and the amino acid sequence exhibits at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity with one of the amino acid sequences. In some embodiments, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprise V having an amino acid sequence selected from any one of SEQ ID NOs 683-704 L Domain, and amino acid sequence and one of said amino acid sequencesIndividual exhibit at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity.
Although selected from V listed above H Domain and V L V of the Domain amino acid sequence H Domain and V L All possible pairings of domains are permissible and within the scope of the present disclosure, but some embodiments still provide V H Domain and V L Certain combinations of domains. Thus, in some embodiments, the anti-CD 33 mAb, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv) comprise V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 43-88, e.g.:
481 and 505;
482 and 506;
483 and 507;
484 and 508;
485 and 509;
486 and 510;
487 and 511;
488 and 512;
489 and 513;
490 and 514;
491 and 515;
492 and 516;
493 and 517;
494 and 518;
495 and 519;
496 and 520;
497 and 521;
498 and 522;
499 and 523;
500 and 524;
501 and 525;
SEQ ID NO. 502 and SEQ ID NO. 526;
503 and 527;
504 and 528;
661 and 683;
662 and 684;
663 and 685;
664 and 686;
665 and 687;
666 and 688;
667 and 689;
668 and 690;
669 and 691;
670 and 692;
671 and 693;
672 and 694;
673 and 695;
674 and 696;
675 and 697;
SEQ ID NO. 676 and SEQ ID NO. 698;
677 and 699;
SEQ ID NO. 678 and SEQ ID NO. 700;
679 and 701;
680 and 702;
SEQ ID NO. 681 and SEQ ID NO. 703;
and
682 SEQ ID NO and 704 SEQ ID NO.
In some embodiments, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprise V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 43-66, e.g.:
481 and 505;
482 and 506;
483 and 507;
484 and 508;
485 and 509;
486 and 510;
487 and 511;
488 and 512;
489 and 513;
490 and 514;
491 and 515;
492 and 516;
493 and 517;
494 and 518;
495 and 519;
496 and 520;
497 and 521;
498 and 522;
499 and 523;
500 and 524;
501 and 525;
SEQ ID NO. 502 and SEQ ID NO. 526;
503 and 527;
and
SEQ ID NO 504 and SEQ ID NO 528.
In some embodiments, the anti-CD 33 mAb, antigen-binding fragment thereof, and synthetic antigen-binding protein (e.g., scFv) comprise V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 67-88, e.g.:
661 and 683;
662 and 684;
663 and 685;
664 and 686;
665 and 687;
666 and 688;
667 and 689;
668 and 690;
669 and 691;
670 and 692;
671 and 693;
672 and 694;
673 and 695;
674 and 696;
675 and 697;
SEQ ID NO. 676 and SEQ ID NO. 698;
677 and 699;
SEQ ID NO. 678 and SEQ ID NO. 700;
679 and 701;
680 and 702;
SEQ ID NO. 681 and SEQ ID NO. 703;
and
682 SEQ ID NO and 704 SEQ ID NO.
In some embodiments, the anti-CLL-1 antibodies, antigen-binding fragments thereof, and synthetic antigen-binding proteins (e.g., scFv) may also comprise a combination of a variable heavy chain domain and a variable light chain domain, wherein the variable heavy chain domain comprises a V having at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to a variable heavy chain amino acid sequence as set forth above H A sequence, and/or wherein the variable light domain comprises a V having at least 90% sequence identity or at least 95%, 96%, 97%, 98% or 99% sequence identity to a variable light domain amino acid sequence set forth above L Sequence. Specific V which may remain in the whole part (i) H And V L Pairing or combining is used to have V with a specific percentage of amino acid sequence identity to these reference sequences disclosed herein H And V L anti-CLL-1 antibodies to domain sequences.
For antibodies therein, antigen binding thereofAll examples, V, of synthetic fragments, and variable heavy and/or light chain domains of synthetic antigen binding proteins (e.g., scFv) defined by a specific percentage of amino acid sequence identity to a reference sequence H And/or V L The domains may retain CDR sequences identical to those present in the reference sequence such that the changes exist only within the framework regions.
Chimeric Antigen Receptor (CAR) and immune effector cells bearing CAR
Also provided herein are chimeric antigen receptors (CARs; as well as transgenic T cell receptors, TCRs) and immune effector cells expressing them, comprising polypeptides as disclosed herein, e.g., as disclosed in tables 2, 3, 12 and 13. A CAR is a recombinant fusion protein comprising: 1) an extracellular ligand binding domain, i.e. an antigen recognition domain, 2) a hinge domain, 3) a transmembrane domain, and 4) a cytoplasmic signaling domain, 5) and optionally a co-stimulatory domain.
Methods for CAR design, delivery and expression and manufacturing clinical-grade CAR-T cell populations are known in the art. CAR designs are typically tailored for each cell type.
The extracellular ligand binding domain of the chimeric antigen receptor recognizes and specifically binds to an antigen (typically a surface expressed antigen of a malignant cell). For example, when the extracellular ligand binding domain has an affinity constant or interaction affinity (K) of about 0.1pM to about 10. Mu.M, or about 0.1pM to about 1. Mu.M, or about 0.1pM to about 100nM D ) Upon binding an antigen, the extracellular ligand binding domain specifically binds the antigen. Methods for determining interaction affinities are known in the art. An extracellular ligand binding domain can also be said to specifically bind a first polymorphic variant of an antigen when the extracellular ligand binding domain selectively binds to the first polymorphic variant of the same antigen relative to a second polymorphic variant of the antigen.
The extracellular ligand binding domain suitable for use in a CAR can be any antigen binding polypeptide, a very large number of which are known in the art. In some cases, the extracellular ligand binding domain is a single chain Fv (scFv). Other antibody-based recognition domains (cAb VHH (camelid antibody variable domain)) and humanized versions thereof, lgNAR VH (shark antibody variable domain) and humanized versions thereof, sdAb VH (single domain antibody variable domain) and "camelized" antibody variable domains are also suitable for use. In some cases, recognition domains based on T Cell Receptors (TCRs), such as single chain TCRs (scTv, single chain double domain TCRs containing vαvβ), are also suitable for use. In some embodiments, the extracellular ligand binding domain is constructed from a native binding partner to the target antigen or a functional fragment thereof. For example, CARs can generally be constructed with a portion of the APRIL protein that targets B Cell Maturation Antigen (BCMA) and ligands for Transmembrane Activator and CAML Interactors (TACI), effectively co-targeting both BCMA and TACI to treat multiple myeloma.
The targeting antigen to which the CAR binds via its extracellular ligand binding domain may be an antigen expressed on malignant myeloid (AML) cells, T cells or other cells. Antigens expressed on malignant myeloid (AML) cells include CD33, FLT3, CD123 and CLL-1. Antigens expressed on T cells include CD2, CD3, CD4, CD5, CD7, TCR alpha (TRAC) and TCR beta. Antigens expressed on malignant plasma cells include BCMA, CS1, CD38, CD79A, CD79B, CD138 and CD19. Antigens expressed on malignant B cells include CD19, CD20, CD21, CD22, CD23, CD24, CD25, CD27, CD38 and CD45.
Typically, the extracellular ligand binding domain is linked to the intracellular domain of the chimeric antigen receptor by a Transmembrane (TM) domain. Peptide hinges connect the extracellular ligand binding domain to the transmembrane domain. The transmembrane domain passes through the cell membrane, anchors the CAR to the T cell surface, and connects the extracellular ligand-binding domain to the cytoplasmic signaling domain, thereby affecting the expression of the CAR on the T cell surface.
The transmembrane domain may be derived from natural or synthetic sources. Where the source is natural, the domain may be derived from any membrane-bound protein or transmembrane protein. For example, the transmembrane region may be derived from (i.e., include at least one or more of) the α, β or ζ chain of a T cell receptor, CD28, CD3 ε, CD45, CD4, CD5, CD8 (e.g., CD8 α, CD8 β), CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD154, KIRDS2, OX40, CD2, CD27, LFA-1 (CD 11a, CD 18), ICOS (CD 278), 4-1BB (CD 137), GITR, CD40, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF 1), CD160, CD19, IL2Rβ, IL2 Rgamma, IL7 Ralpha, ITGA1, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11D, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11B, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, TNFR2, DNAM1 (CD 226), SLAMF4 (CD 244, 2B 4), CD84, CD96 (Tactive), CEACAM1, CRTAM, ly9 (CD 229), CD160 (BY 55), PSGL1, CD100 (SEMA 4D), SLAMF6 (NTB-A, ly), SLAMF1, CD150, IPO-3), BLASME (SLAMF 8), PLG (CD 162), LTBR and PAG/PAG. Alternatively, the transmembrane domain may be synthetic and comprise predominantly hydrophobic amino acid residues (e.g. leucine and valine). In some cases, triplets of phenylalanine, tryptophan and valine will be found at each end of the synthetic transmembrane domain. In some embodiments, the transmembrane domain is derived from the T cell surface glycoprotein CD8 a chain subtype 1 precursor (NP 001139345.1) or CD28. Short oligopeptides or polypeptide linkers (e.g., 2 to 10 amino acids in length) can form a link between the transmembrane domain and the endoplasmic reticulum domain of the CAR. In some embodiments, the CAR has more than one transmembrane domain, which may be a repeat of the same transmembrane domain, or may be a different transmembrane domain.
NK cells express a number of Transmembrane (TM) adaptors that emit activation signals, which are triggered by association with an activation receptor. This provides NK cell specific signal enhancement via engineering of the TM domain from activating the receptor and thus utilizing endogenous adaptors. The TM adapter may be any endogenous TM adapter capable of emitting an activation signal. In some embodiments, the TM adaptor may be selected from fce1γ (ITAMx 1), cd3ζ (ITAMx 3), DAP12 (ITAMx 1), or DAP10 (yxmm/YINM), NKG2D, fc γriiia, NKp44, NKp30, NKp46, actKIR, NKG2C, CD8 α, and IL15Rb.
The CAR may further comprise a hinge region between the extracellular ligand binding domain and the transmembrane domain. The term "hinge region" (equivalent to a "hinge" or "spacer") generally means any oligopeptide or polypeptide that functions to connect a transmembrane domain to an extracellular ligand binding domain. In particular, the hinge region serves to provide more flexibility and accessibility to the extracellular ligand binding domain, and may confer stability to efficient CAR expression and activity. The hinge region may comprise up to 300 amino acids, preferably 10 to 100 amino acids, and most preferably 25 to 50 amino acids. The hinge region may be derived from all or part of naturally occurring molecules such as CD28, 4-1BB (CD 137), OX-40 (CD 134), CD3 ζ, T cell receptor alpha or beta chain, CD45, CD4, CD5, CD8a, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, ICOS, CD154; or derived from all or part of the antibody constant region. In some embodiments, for example, the hinge sequence is derived from a CD8a molecule or a CD28 molecule. Alternatively, the hinge region may be a synthetic sequence corresponding to a naturally occurring hinge sequence, or the hinge region may be a fully synthetic hinge sequence. In one embodiment, the hinge domain comprises a portion of a human CD8a, fcyriii a receptor, or IgGl, and has at least 80%, 90%, 95%, 97%, or 99% sequence identity thereto.
Upon antigen recognition, the cytoplasmic signaling domain signals the immune effector cell, thereby activating at least one normal effector function of the immune effector cell. For example, the effector function of a T cell may be cytolytic activity or helper activity (including secretion of cytokines). Although it is generally possible to use the entire cytoplasmic signaling domain, in many cases the entire chain need not be used. In the case of using a truncated portion of a cytoplasmic signaling domain, such a truncated portion may be used in place of the complete strand, so long as it transduces effector functions.
The cytoplasmic signaling sequence that acts in a stimulatory manner to regulate primary activation of the TCR complex may contain a signaling motif known as an immune receptor tyrosine-based activation motif (ITAM). Examples of ITAM-containing cytoplasmic signaling sequences include those derived from CD8, CD3 ζ, CD3 δ, CD3 γ, CD3 ε, CD32 (fcγriia), DAP10, DAP12, CD79a, CD79b, fcγri γ, fcγriii γ, fcεri β (FCERIB), and fcεri γ (FCERIG).
First generation CARs typically have cytoplasmic signaling domains from the CD3 chain, which are the primary transmitters of signals from endogenous TCRs. The second generation CARs add cytoplasmic signaling domains from various costimulatory protein receptors (e.g., CD28, 4-1BB, ICOS) to the cytoplasmic signaling domain of the CAR to provide additional signals to T cells.
The "costimulatory domain" derives from the intracellular signaling domain of a costimulatory protein, which enhances cytokine production, proliferation, cytotoxicity, and/or persistence in vivo. Preclinical studies have shown that second generation CAR designs improve the anti-tumor activity of T cells. Recently, third and later generation CARs have incorporated multiple co-stimulatory domains to further enhance potency. T cells transplanted with these CARs have shown improved expansion, activation, persistence, and tumor eradication efficiency independent of co-stimulatory receptor/ligand interactions.
For example, the cytoplasmic signaling domain of the CAR can be designed to comprise the signaling domain (e.g., cd3ζ) itself, or in combination with one or more of any other desired cytoplasmic domains useful in the context of the CAR. For example, the cytoplasmic domain of the CAR can comprise a signaling domain (e.g., cd3ζ) chain portion and a costimulatory signaling region. A costimulatory signaling region refers to the portion of the CAR that comprises the intracellular domain of a costimulatory molecule. Examples of such molecules include CD27, CD28, 4-1BB (CD 137), OX40, CD30, CD40, ICOS, LFA-1, CD2, CD7, LIGHT, NKG2C, B-H3, and ligands that specifically bind to CD83, CD8, CD4, b2c, CD80, CD86, DAP10, DAP12, myD88, BTNL3, and NKG 2D.
In some embodiments, the cytoplasmic signaling domain is a CD3 zeta (cd3ζ) signaling domain. In some embodiments, the costimulatory domain comprises the cytoplasmic domain of CD28, 4-1BB, or a combination thereof. In some cases, the costimulatory signaling region comprises 1, 2, 3, or 4 cytoplasmic domains of one or more intracellular signaling and/or costimulatory molecules.
One or more co-stimulatory signaling domains may contain one or more mutations that enhance signaling in the cytoplasmic domains of CD28 and/or 4-1 BB. In some embodiments, the disclosed CARs comprise a co-stimulatory signaling region comprising a mutant form of the cytoplasmic domain of CD28 having altered phosphorylation at Y206 and/or Y218. In some embodiments, the disclosed CAR comprises a attenuating mutation at Y206 that will reduce the activity of the CAR. In some embodiments, the disclosed CAR comprises a attenuating mutation at Y218 that will reduce expression of the CAR. Any amino acid residue (e.g., alanine or phenylalanine) may be substituted for tyrosine to effect attenuation. In some embodiments, the tyrosine at Y206 and/or Y218 is substituted with a pseudophosphate residue. In some embodiments, the disclosed CARs comprise a substitution of Y206 by a pseudophosphate residue that will increase the activity of the CAR. In some embodiments, the disclosed CARs comprise a substitution of Y218 for a pseudophosphate residue that will increase expression of the CAR. For example, the pseudophosphate residue may be phosphotyrosine. In some embodiments, the CAR may contain a combination of a phosphoramidate amino acid and one or more substitutions with non-phosphorylable amino acids in different residues of the same CAR. For example, the CAR may contain an alanine or phenylalanine substitution in Y209 and/or Y191 plus a pseudophosphoric acid substitution in Y206 and/or Y218.
In some embodiments, the disclosed CARs comprise one or more 4-1BB domains with mutations that enhance binding to specific TRAF proteins, such as TRAF1, TRAF2, TRAF3, TRAF4, TRAF5, TRAF6, or any combination thereof. In some cases, 41BB mutations enhance TRAF1 and/or TRAF 2-dependent proliferation and survival of T cells, e.g., by NF-kB. In some cases, the 4-1BB mutation enhances TRAF 3-dependent antitumor efficacy, e.g., by IRF7/INFβ. Thus, the disclosed CARs may comprise one or more cytoplasmic domains of 4-1BB having at least one mutation in these sequences that enhances TRAF binding and/or enhances nfkb signaling.
As also disclosed herein, TRAF proteins can in some cases enhance CAR T cell function independent of nfkb and 4-1BB. For example, TRAF proteins may in some cases enhance CD28 co-stimulation in T cells. Thus, also disclosed herein are immune effector cells that co-express a CAR and one or more TRAF proteins (e.g., TRAF1, TRAF2, TRAF3, TRAF4, TRAF5, TRAF6, or any combination thereof). In some cases, the CAR is any CAR that targets a tumor antigen. For example, first generation CARs typically have an intracellular domain from the CD3 chain, while second generation CARs add intracellular signaling domains from various costimulatory protein receptors (e.g., CD28, 4-1BB, ICOS) to the cytoplasmic signaling domain of the CAR to provide additional signals to T cells. In some cases, the CAR is a disclosed CAR having enhanced 4-1BB activation.
Variations in the CAR component may be advantageous, depending on the type of CAR-expressing cell.
For example, in NK cells, in some embodiments, the transmembrane domain may be a sequence associated with NKG2D, fc γriiia, NKp44, NKp30, NKp46, actKIR, NKG2C, or CD8 a. In certain embodiments, the NK cell is an ML-NK or CIML-NK cell, and the TM domain is CD8 alpha. Certain TM domains that do not function well in NK cells can generally function in a subset; for example, CD 8. Alpha. Operates in ML-NK, but generally does not operate in NK cells.
Similarly, in NK cells, in some embodiments, the one or more intracellular signaling domains may be any one or more co-activating receptors capable of functioning in NK cells, such as, for example, CD28, CD137/41BB (TRAF, NFkB), CD134/OX40, CD278/ICOS, DNAM-1 (Y motif), NKp80 (Y motif), 2B4 (SLAMF): ITSM, CRACC (CS 1/SLAMF 7): ITSM, CD2 (Y motif, MAPK/Erk), CD27 (TRAF, NFkB), or integrins (e.g., various integrins).
Similarly, in NK cells, in some embodiments, the intracellular signaling domain may be a cytokine receptor capable of functioning in NK cells. For example, the cytokine receptor may be a cytokine receptor associated with persistence, survival or metabolism, such as IL-2/15Rbyc: jak1/3, STAT3/5, PI3K/mTOR, MAPK/ERK. As another example, the cytokine receptor may be an activation-related cytokine receptor, such as IL-18R:: NFkB. As another example, the cytokine receptor may be a cytokine receptor associated with IFN-gamma production, such as IL-12R:: STAT4. As another example, the cytokine receptor may be a cytokine receptor associated with cytotoxicity or persistence, such as IL-21R: jak3/Tyk2, or STAT3. As another example, the intracellular signaling domain may be a TM adaptor, such as fcer1γ (ITAMx 1), cd3ζ (ITAMx 3), DAP12 (ITAMx 1), or DAP10 (YxxM/YINM). As another example, the CAR intracellular signaling domain (also referred to as an inner domain) may be derived from a co-stimulatory molecule of the CD28 family (e.g., CD28 and ICOS) or of the Tumor Necrosis Factor Receptor (TNFR) gene family (e.g., 4-1BB, OX40, or CD 27). TNFR family members signal by recruiting TRAF proteins and are involved in cell activation, differentiation and survival. Certain signaling domains that do not function well in all NK cells can generally function in a subset; for example, CD28 or 4-1BB operates in ML-NK.
Methods of making CARs and CAR-bearing cells
Chimeric Antigen Receptor (CAR) constructs encoding chimeric receptors can be prepared in a conventional manner. Since in most cases the native sequence is used, the native gene is optionally isolated and manipulated (e.g., when using type II receptors, the immune signaling receptor components may have to be inverted) to allow for proper ligation of the various components. Thus, the nucleic acid sequences encoding the N-terminal and C-terminal proteins of the chimeric receptor can be isolated by employing Polymerase Chain Reaction (PCR) using appropriate primers that result in the deletion of undesired gene portions. Alternatively, restriction enzyme cuts of cloned genes may be used to generate chimeric constructs. In either case, the sequences may be selected to provide restriction sites that are blunt ended or have complementary overlap.
The various manipulations used to prepare the chimeric construct may be performed in vitro, and in particular embodiments, the chimeric construct is introduced into a vector for cloning and expression in an appropriate host using standard transformation or transfection methods. Thus, after each manipulation, the resulting construct from the ligation of the DNA sequences is cloned, the vector is isolated, and the sequences are screened to ensure that the sequences encode the desired chimeric receptor. Sequences may be screened by restriction analysis, sequencing, and the like.
The chimeric construct may be introduced into immune effector cells as naked DNA or in a suitable vector. Methods for stably transfecting immune effector cells by electroporation using naked DNA are known in the art. Naked DNA generally refers to DNA encoding a chimeric receptor that is contained in a plasmid expression vector in a suitable orientation for expression.
Alternatively, the chimeric construct may be introduced into an immune cell (e.g., T cell) using a viral vector (e.g., a retroviral vector, an adenoviral vector, an adeno-associated viral vector, or a lentiviral vector). Suitable vectors are non-replicative in immune effector cells of a subject. A number of viral-based vectors are known in which the number of copies of virus maintained in a cell is sufficiently low to maintain viability of the cell. Illustrative vectors include the pFB-neo vector (STRATAGENTE TM ) And vectors based on HIV, SV40, EBV, HSV or BPV. Once it is established that transfected or transduced immune effector cells are capable of expressing the chimeric receptor as a surface membrane protein at the desired modulation and at the desired level, it can be determined whether the chimeric receptor functions in the host cell to provide the desired signal induction (e.g., the production of Rantes, mip1- α, GM-CSF upon stimulation with the appropriate ligand).
The engineered CARs can be introduced into CAR-bearing immune effector cells using retroviruses that efficiently and stably integrate nucleic acid sequences encoding chimeric antigen receptors into the target cell genome. Other methods known in the art include, but are not limited to, lentiviral transduction, transposon-based systems, direct RNA transfection, and CRISPR/Cas systems (e.g., type I, type II, or type III systems using suitable Cas proteins such as Cas3, cas4, cas5e (or CasD), cash, cas6e, cas6f, cas7, cas8a1, cas8a2, cas8b, cas8c, cas9, cas10, cas1 Od, casF, casG, casH, csy1, csy2, csy3, cse1 (or CasA), cse2 (or CasB), cse3 (or CasE), cse4 (or CasC), csc1, csc2, csa5, csn2, csm3, csm4, csm5, csm6, cmr1, cmr3, cmr4, cmr5, cmr6, b1, csb2, csb3, csx17, csx10, csx3, csx15, and the like). Zinc Finger Nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) can also be used. See, e.g., shearer RF and sacunders DN, "Experimental design for stable genetic manipulation in mammalian cell lines: lentivirus and alternatives [ experimental design of stable gene manipulation in mammalian cell lines: lentivirus and surrogate ], "Genes Cells [ gene to cell ] 1 month 2015; 20 (1):1-10.
The amino acid sequences of selected components useful in constructing the CAR are disclosed in table 1 below.
TABLE 1 amino acid sequences of selected CAR components.
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Cell-specific changes
The CAR components and methods of construction disclosed above are suitable for use with T cells and other immune effector cells, but are not exhaustive. Certain variants are useful for subpopulations of cells and are known in the art.
For example, in NK cells, the TM domain may be selected from or adapted from NKG2D, fc γriiia, NKp44, NKp30, NKp46, actKIR, NKG2C or CD8 a. NK cells also express a number of transmembrane adaptors that trigger via association with activating receptors, providing NK cell specific signal enhancement. For example, the TM adaptor may be selected from or adapted from FceR1γ (ITAMx 1), CD3 ζ (ITAMx 3), DAP12 (ITAMx 1), or DAP10 (YxxM/YINM). In certain embodiments, the TM domain and the adapter may be paired, for example: NKG2D and DAP10, fcγriiia and cd3ζ or fcer1γ, NKp44 and DAP12, NKp30 and cd3ζ or fcer1γ, NKp46 and cd3ζ or fcer1γ, actKIR and DAP12, and NKG2C and DAP12.
In certain embodiments, in NK cells, the hinge domain may be selected from or adapted from, for example, NKG2, tmα, or CD8.
In certain embodiments, in NK cells, the intracellular signaling domain and/or co-stimulatory domain may comprise one or more of the following: CD137/41BB (TRAF, NFkB), DNAM-1 (Y motif), NKp80 (Y motif), 2B4 (SLAMF): ITSM, CRACC (CS 1/SLAMF 7): ITSM, CD2 (Y motif, MAPK/Erk), CD27 (TRAF, NFkB); one or more integrins (e.g., a plurality of integrins); cytokine receptors associated with persistence, survival or metabolism, such as IL-2/15Rbyc: jak1/3, STAT3/5, PI3K/mTOR, and MAPK/ERK; cytokine receptors associated with activation, such as IL-18R:: NFkB; cytokine receptors associated with IFN-gamma production, such as IL-12R:: STAT4; cytokine receptors associated with cytotoxicity or persistence, such as IL-21R: jak3/Tyk2, or STAT3; and a TM adaptor as disclosed above. In some embodiments, the NK cell CAR comprises three signaling domains, one TM domain, and optionally one TM adapter.
The choice of co-stimulatory domain may also depend on the phenotype or subtype of NK cells; for example, in some experiments 4-1BB may be effective as a co-stimulatory domain in memory-like (ML) NK cells (including CIML), but less effective in NK cells. In addition, signaling domains that can be utilized that are more selectively expressed in ML NK cells include DNAM-1, CD137, and CD2.
Immune effector cells
Immune effector cells as disclosed herein may include T cells, NK cells, iNKT cells, and other cells, such as macrophages and subtypes thereof.
Any of these immune effector cells can be transduced with a CAR using techniques known in the art. The resulting CAR-bearing immune effector cells can be used in immunotherapy of disease (e.g., cancer) by Adoptive Cell Transfer (ACT) into a subject in need thereof. Immune effector cells bearing CARs include CAR-T cells, CAR-NK cells (and subtypes thereof, such as CAR-ML NK cells and CAR-CIML), CAR-iNKT cells, and CAR macrophages.
The immune effector cells used for ACT may be autologous or allogeneic. In some embodiments, the use of allogeneic cells allows for intentional polymorphic mismatches between the donor and recipient, which provides certain advantages discussed below.
T cell
T cells are immune cells that express a T Cell Receptor (TCR) on their surface. Effector T cells include cytotoxic (cd8+) T cells, helper (cd4+) T cells, virus-specific cytotoxic T cells, memory T cells, γδ T cells.
The T cells may be primary T cells or may be derived from progenitor cells. T cells may be derived from a variety of sources, including peripheral or umbilical cord blood cells, stem cells, or induced pluripotent stem cells (ipscs). Methods for enriching/isolating, differentiating and otherwise producing T cells are known in the art.
iNKT cells
Constant natural killer T cells (also known as iNKT cells or type I NKT cells) represent a diverse population of lymphocytes characterized by expression of constant T cell receptor alpha chains and certain TCR beta chains (vα24-jα18 in combination with vβ11). iNKT TCR-mediated responses are limited by CD1d, a member of the non-polymorphic CD1 antigen presenting protein family, which promotes presentation of endogenous and pathogen-derived lipid antigens to the TCR. The prototype ligand for the constant receptor was α -galactosylceramide (αgalcer). iNKT will amplify after binding of the constant TCR to CD1d- αgalcer. The CD1d gene is singlet and is expressed by only a few cell types, which limits the potential toxicity of NKT cells in autologous or allogeneic environments.
NK cells
Natural Killer (NK) cells have traditionally been considered to be innate immune effector lymphocytes that mediate host defenses and anti-tumor immune responses against pathogens by targeting and eliminating abnormal or stressed cells, not by antigen recognition or prior sensitization, but by integrating signals from activating and inhibitory receptors. Natural Killer (NK) cells are T cell substitutes for allogeneic cell immunotherapy because they are safe to administer without significant toxicity, do not cause graft versus host disease (GvHD), naturally recognize and eliminate malignant cells, and are useful in cell engineering.
The NK cells may be primary NK cells or may be derived from progenitor cells. NK cells may be derived from a variety of sources, including peripheral or umbilical cord blood cells, stem cells, or induced pluripotent stem cells (ipscs). Methods of enriching/isolating, differentiating and otherwise producing NK cells are known in the art.
Memory-like NK cells
In addition to its innate cytotoxic and immunostimulatory activities, NK cells also constitute heterogeneous and multifunctional cell subsets, including persisting memory-like NK populations that produce robust recall responses. ML-NK cells can be produced naturally or artificially by stimulation of pro-inflammatory cytokines or activation of receptor pathways. ML-NK cells produced by cytokine activation have been used clinically in the context of leukemia immunotherapy.
CD56, ki-67, NKG2A increase and activation receptors NKG2D, NKp and NKG 44 increase have been observed in vivo differentiated ML NK cells. In addition, in vivo differentiation showed a slight decrease in median expression of CD16 and CD11 b. An increase in frequency of TRAIL, CD69, CD62L, NKG a and NKp30 positive NK cells, and a decrease in frequency of cd27+ and cd127+ NK cells was observed in ML NK cells compared to both ACT and BL NK cells. Finally, unlike ML NK cells differentiated in vitro, ML NK cells differentiated in vivo do not express CD25.
Cytokine-induced memory-like natural killer cells (CIML-NK)
NK cells can be induced to acquire a memory-like phenotype, for example, by pre-activation with a combination of cytokines such as interleukin-12 (IL-12), IL-15 and IL-18. These cytokine-induced memory-like (CIML) NK cells (CIML-NK or CIML) exhibit enhanced responses upon re-stimulation with cytokines or triggering via activating receptors. CIML NK cells can be produced by activation with cytokines (e.g., IL-12, IL-15, and IL-18) and related family members, or functional fragments thereof, or fusion proteins comprising functional fragments thereof.
CIML NK cells can be identified by their production method. CIML cells can be produced by differentiated cytokine-activated (i.e., CIML) NK cells.
CIML NK cells typically exhibit differential cell surface protein expression patterns compared to traditional NK cells. Such expression patterns are known in the art and may comprise, for example, increased CD56 in CIML NK cells, CD56 sub-population CD56 dark, CD56 sub-population CD56 light, CD16, CD94, NKG2A, NKG2D, CD L, CD25, NKp30, NKp44 and NKp46 (as compared to control NK cells) (see, for example, romee et al Sci transfer Med. [ science transformation of science ]2016, 9, 21, 8 (357): 357). Memory-like (ML) and cytokine-induced memory-like (CIML) NK cells can also be identified by observed in vitro and in vivo properties such as enhanced effector functions such as cytotoxicity, improved persistence, increased IFN- γ production, etc.
NK cells can be activated using cytokines such as IL-12/15/18. NK cells can be incubated in the presence of cytokines for a sufficient amount of time to form cytokine-induced memory-like (CIML) NK cells. Such techniques are known in the art.
CD33, FTL-3 and CLL-1 specific Chimeric Antigen Receptors (CARs)
CARs typically incorporate an antigen recognition domain of a single chain variable fragment (scFv) from a monoclonal antibody (mAb) that has a transmembrane signaling motif involved in lymphocyte activation (Sadelain M et al Nat Rev Cancer natural comment 2003 3:35-45). Disclosed herein are CD33, FTL-3 and CLL-1 specific Chimeric Antigen Receptors (CARs) that can be expressed in immune effector cells to enhance anti-tumor activity against tumor cells expressing CD33, FTL-3 and CLL-1.
As discussed above, the disclosed CAR generally comprises: an extracellular ligand binding domain, a hinge domain, a transmembrane domain, a cytoplasmic signaling domain, and optionally a co-stimulatory domain. The extracellular ligand binding domain comprises a CD33 binding region and is responsible for antigen recognition. In another embodiment, the extracellular ligand binding domain comprises a FLT3 binding region. In yet another embodiment, the extracellular ligand binding domain comprises a CLL-1 binding region. The transmembrane domain connects the extracellular ligand binding domain to the cytoplasmic signaling domain and resides within the cell membrane when expressed by the cell. Upon antigen recognition, the cytoplasmic signaling domain transmits an activation signal to immune effector cells. For example, the cytoplasmic signaling domain may optionally contain a costimulatory protein domain capable of enhancing the activation of T cells by T cell receptors, such as CD28, 41BB and ICOS.
Antibodies to
Provided herein are antibodies comprising the polypeptides disclosed herein. In some embodiments, the antibodies comprise V disclosed herein H Chain and V L A chain.
Different forms of the disclosed antibodies are contemplated herein. For example, antibodies may have human frameworks and constant regions of isotypes IgA, igD, igE, igG and IgM (more particularly IgG1, igG2, igG3, igG 4) and in some cases have different mutations that alter Fc receptor function or prevent Fab arm exchange, or antibody fragments, such as F (ab') 2 fragments, F (ab) fragments, single chain Fv fragments (scFv), and the like.
In certain embodiments, the antibodies provided herein are human antibodies. Various techniques known in the art may be used to produce human antibodies. For example, human antibodies can also be produced by isolating Fv clone variable domain sequences selected from a humanized phage display library. Such variable domain sequences can then be combined with the desired human constant domain.
Antibodies as provided herein can be chimeric antibodies, for example, comprising a non-human variable region (e.g., a variable region derived from a mouse, rat, hamster, rabbit, or non-human primate (e.g., monkey)) and a human constant region, or "class switching" antibodies, wherein the class or subclass has been altered from the class or subclass of the parent antibody.
The antibody as provided herein may be a humanized antibody. Typically, non-human antibodies are humanized to reduce immunogenicity to humans, while retaining the specificity and affinity of the parent non-human antibody. Typically, a humanized antibody comprises one or more variable domains in which the HVRs (e.g., CDRs) (or portions thereof) are derived from a non-human antibody and the FRs (or portions thereof) are derived from a human antibody sequence. The humanized antibody optionally will also comprise at least a portion of a human constant region. In some embodiments, some FR residues in a humanized antibody are substituted with corresponding residues from a non-human antibody (e.g., an antibody from which HVR residues are derived), e.g., to restore or improve antibody specificity or affinity.
The antibodies disclosed herein may also be bispecific or trispecific-i.e., they comprise an antigen recognition domain comprising one of the polypeptides disclosed herein and one or more other antigen recognition domains that bind to another antigen. For example, one arm of an antibody may bind to a polymorphism of an antigen on AML cells, and the other arm may bind to CD3 or another T cell target to bring T cells close to tumor cells. In the case of a trispecific antibody, the antibody will also bind to another target on the T cell (e.g., CD 28) to enhance the activity and persistence of the recruited T cell.
In some embodiments, the humanized antibody further comprises a human acceptor framework, such as a human immunoglobulin framework or a human consensus framework, in addition to the variable region. Human framework regions useful for humanization include, but are not limited to, framework regions selected using a "best fit" method, framework regions derived from a specific subset of human antibody consensus sequences for light or heavy chain variable regions, human mature (somatic mutated) framework regions or human germline framework regions, and framework regions derived from screening FR libraries.
In certain embodiments, the antibodies provided herein are multispecific antibodies, e.g., bispecific antibodies. Multispecific antibodies are monoclonal antibodies that have binding specificities for at least two different sites. For example, one of the binding specificities is for CD33 and the other is for any other antigen. In certain embodiments, the bispecific antibody can bind to two different epitopes of the same antigen. Bispecific antibodies can also be used to localize cytotoxic agents to cells expressing a target antigen. Bispecific antibodies can be prepared as full length antibodies or antibody fragments. Techniques for preparing multispecific antibodies include, but are not limited to, recombinant co-expression of two immunoglobulin heavy chain-light chain pairs with different specificities, "knob-in-hole" engineering, engineering of electrostatic targeting for preparing antibody Fc heterodimer molecules, crosslinking two or more antibodies or fragments, producing bispecific antibodies using leucine zippers, preparing bispecific antibody fragments using "diabody" techniques, and using single chain Fv (sFv) dimers.
Amino acid sequence variants of the antibodies provided herein are contemplated. For example, it may be desirable to improve the binding affinity and/or other biological properties of antibodies. Amino acid sequence variants of antibodies can be prepared by introducing appropriate modifications to the nucleotide sequence encoding the antibody or by peptide synthesis. Such modifications include, for example, deletions from and/or insertions into and/or substitutions of residues within the amino acid sequence of an antibody. Any combination of deletions, insertions, and substitutions may be made to obtain the final construct, provided that the final construct has the desired characteristics, such as antigen binding.
The target sites for substitution mutagenesis include variable and framework regions. Amino acids can be grouped according to common side chain characteristics:
(1) Hydrophobicity: norleucine, met, ala, val, leu, he;
(2) Neutral hydrophilicity: cys, ser, thr, asn, gln;
(3) Acid: asp, glu;
(4) Alkaline: his, lys, arg;
(5) Residues that affect chain orientation: gly, pro;
(6) Aromatic: trp, tyr, phe.
Amino acid substitutions may be introduced into the antibody of interest and the products screened for a desired activity, such as retained/improved antigen binding, reduced immunogenicity, or improved ADCC or CDC. Conservative substitutions are known in the art and are preferred. Non-conservative substitutions will require the exchange of members of one of these classes for members of the other class.
Antibodies may also contain modifications to the glycan chains to replace certain residues, such as Asn297. For example, antibodies can be engineered or treated to defucosylate to improve ADCC.
Antibodies comprising the CDRs, variable heavy and light chains disclosed herein can be prepared by methods known in the art.
For example, the variable antibody domains can be cloned into an IgG expression vector (IgG conversion). The PCR amplified DNA fragments of the heavy and light chain V domains can be inserted in-frame into a recipient mammalian expression vector containing, for example, a human IgG1 constant heavy chain. Antibody expression can be driven by the MPSV promoter and transcription can be terminated by a synthetic poly a signal sequence located downstream of the CDS.
Recombinant methods and compositions can be used to produce antibodies. Nucleic acids encoding the antibodies described herein are provided. Such nucleic acids may encode an amino acid sequence comprising a VL of an antibody and/or an amino acid sequence comprising a VH of an antibody (e.g., a light chain and/or a heavy chain of an antibody). Expression vectors comprising (i.e., transformed with) such nucleic acids, as well as host cells comprising such nucleic acids, are provided. In one such embodiment, the host cell comprises (1) a vector comprising nucleic acid encoding an amino acid sequence comprising VL and an amino acid sequence comprising VH, or (2) a first vector comprising nucleic acid encoding an amino acid sequence comprising VL of an antibody and a second vector comprising nucleic acid encoding an amino acid sequence comprising VH of the antibody.
The host cell may be eukaryotic, such as Chinese Hamster Ovary (CHO) cells or lymphocytes (e.g., Y0, NS0, sp20 cells). Host cells comprising nucleic acid encoding the antibody may be cultured under conditions suitable for expression, and the antibody recovered from the host cells or from the culture medium.
Suitable host cells for cloning or expressing the antibody-encoding vectors include other prokaryotic or eukaryotic cells described herein. For example, antibodies can be produced in bacteria such as E.coli (E.coli), particularly when glycosylation and Fc effector function are not required. In addition to prokaryotes, eukaryotic microbes (such as filamentous fungi or yeast) are suitable cloning or expression hosts for vectors encoding antibodies, including fungal and yeast strains whose glycosylation pathways have been "humanized" to produce antibodies with a partially or fully human glycosylation pattern. Additional suitable host cells for expressing glycosylated antibodies are also derived from multicellular organisms (invertebrates and vertebrates). Examples of invertebrate cells include plant cells and insect cells. A number of baculovirus strains have been identified which can be used in combination with insect cells, in particular for transfection of Spodoptera frugiperda (Spodoptera frugiperda) cells. Plant cell cultures may also be used as hosts.
In some embodiments, the dissociation constant (Kd) of an antibody provided herein is<1μΜ、<100nM、<50nM、<10nM、<5nM、<1nM、<0.1nM、<0.01nM or<0.001nM, and optionally>10 -13 M (e.g. 10 -8 M or less, e.g. 10 -8 M to 10 -13 M, e.g. 10 -9 M to 10 -13 M). In one embodiment, kd is measured by radiolabeled antigen binding assays (RIA) using Fab versions of antibodies of interest and antigens thereof, or using surface plasmon resonance assays (e.g., WO 2015089344).
Antibody-drug conjugates
Also provided herein are immunoconjugates comprising an antibody or antigen-binding fragment thereof as disclosed herein conjugated to one or more drugs (e.g., a cytotoxic agent, such as a chemotherapeutic agent, a growth inhibitory agent, a toxin, or a radioisotope). Immunoconjugates allow targeted delivery of drugs or other cytotoxic agents to tumors, increasing therapeutic index by maximizing efficacy and minimizing off-target toxicity. Antibody-drug conjugates (ADCs) disclosed herein include those having anti-cancer activity. The antibody may be covalently attached to the drug moiety through a linker.
Exemplary embodiments of the ADC include: an antibody (Ab) or antigen binding fragment thereof that targets tumor cells, a cytotoxic moiety (such as drug (D)), and a linker moiety (L) that attaches the Ab to D. In some embodiments, the antibody is attached to the linker moiety (L) by one or more amino acid residues (e.g., lysine and/or cysteine).
The ADC may have formula I:
Ab-(L-D) p
wherein:
ab is an antibody or antigen-binding fragment thereof as disclosed herein;
l is a linker;
d is a drug; and is also provided with
p is from about 1 to about 20.
An antibody (Ab) may comprise a polypeptide disclosed herein.
The pharmaceutical moiety (D) of the ADC may comprise any compound, moiety or group having cytotoxic or cytostatic effect, or may be a diagnostic or detectable agent.
The linker (L) is a bifunctional or multifunctional moiety having reactive functional groups for attachment to drugs and antibodies, for example. The linker may have a functional group capable of reacting with the free cysteine present on the antibody to form a covalent bond, or a functional group capable of reacting with the electrophilic group present on the antibody. The linker may be susceptible to cleavage (cleavable linker) under conditions where the compound or antibody remains active, such as acid-induced cleavage, light-induced cleavage, peptidase-induced cleavage, esterase-induced cleavage, and disulfide cleavage. Alternatively, the linker may be substantially resistant to cleavage (e.g., a stable linker or a non-cleavable linker). In some aspects, the linker is a pre-charged linker, a hydrophilic linker, or a dicarboxylic acid-based linker.
Examples of cleavable linkers include acid labile linkers (e.g., comprising hydrazones), protease sensitive (e.g., peptidase sensitive) linkers, photolabile linkers, or disulfide-containing linkers. The joint may be, for example, any of the following: n-succinimidyl-4- (2-pyridyldithio) 2-sulfo-butanoate (sulfo-SPDB), N-succinimidyl-3- (2-pyridyldithio) propanoate (SPDP), N-succinimidyl-4- (2-pyridyldithio) pentanoate (SPP), N-succinimidyl-4- (2-pyridyldithio) butanoate (SPDB), N-Succinimidyl Iodoacetate (SIA), N-succinimidyl (4-iodoacetyl) aminobenzoate (SIAB), maleimide PEG NHS, N-succinimidyl-4- (maleimidomethyl) cyclohexanecarboxylate (SMCC), N-sulfosuccinimidyl-4- (maleimidomethyl) cyclohexanecarboxylate (sulfo-SMCC), and 2, 5-dioxopyrrolidin-l-yl 17- (2, 5-dioxo-2, 5-dihydro-1H-pyrrol-l-yl) -5,8,11, 14-tetraoxo-4, 10-tetraoxo-5, 14-tetraoxo-5, 10-tetrakis-1-heptadecade (CXl-heptadecade).
The number of drug moieties (e.g., p) that can be conjugated to an antibody can be limited by the number of free cysteine residues (which can be naturally occurring or incorporated into the antibody amino acid sequence, or generated using reducing conditions prior to conjugation). In some embodiments, p may be 1 to 10, 2 to 8, or 2 to 5. In some embodiments, p is 3 to 4.
In some embodiments, drug moiety (D) may be selected from an anticancer agent, an antihemorrhagic agent, an autoimmune therapeutic agent, an anti-inflammatory agent, an antifungal agent, an antibacterial agent, an antiparasitic agent, an antiviral agent, an anesthetic agent, a cytotoxin, or a radioactive toxin.
In some embodiments, D may be maytansinoids, V-atpase inhibitors, pro-apoptotic agents, bcl2 inhibitors, MCL1 inhibitors, HSP90 inhibitors, IAP inhibitors, mTor inhibitors, microtubule stabilizing agents, microtubule destabilizing agents, auristatin (auristatin), dolastatin (dolastatin), metAP (methionine aminopeptidase), protein nuclear export CRM1 inhibitors, DPPIV inhibitors, proteasome inhibitors, inhibitors of phosphoryl transfer reactions in mitochondria, protein synthesis inhibitors, kinase inhibitors, CDK2 inhibitors, CDK9 inhibitors, kinesin inhibitors, HDAC inhibitors, DNA damaging agents, DNA alkylating agents, DNA intercalating agents, DNA minor groove adhesives, and DHFR inhibitors.
In some embodiments, drug (D) may be an anticancer agent. Anticancer agents include and D can be, for example:
1) Inhibitors or modulators of proteins involved in one or more DNA Damage Repair (DDR) pathways, such as:
Parp1/2, including but not limited to: olaparib, nilaparib, lu Kapa rib;
b. checkpoint kinase 1 (CHK 1), including but not limited to: UCN-01, AZD7762, PF477736, SCH900776, MK-8776, LY2603618, V158411, and EXEL-9844;
c. checkpoint kinase 2 (CHK 2), including but not limited to: PV1019, NSC 109555, and VRX0466617;
d. dual CHK1/CHK2, including but not limited to: XL-844, AZD7762, and PF-473336;
wee1, including but not limited to: MK-1775 and PD0166285;
atm, including but not limited to KU-55933;
DNA-dependent protein kinases including, but not limited to NU7441 and M3814; and
h. additional proteins involved in DDR;
2) Inhibitors or modulators of one or more immune checkpoints, including but not limited to:
PD-1 inhibitors such as nivolumab (OPDIVO), pembrolizumab (KEYTRUCDA), pituzumab (CT-011) and AMP-224 (AMPLIMMUNE);
PD-L1 inhibitors such as Abilizumab (TECENTRIQ), avenumab (Bavencio), dewaruzumab (Imfinzi), MPDL3280A (Tecentriq), BMS-936559 and MEDI4736;
c. anti-CTLA-4 antibodies, such as ipilimumab (YERVOY) and CP-675,206 (TREMELIMUMAB);
an inhibitor of d.T cellular immunoglobulin and mucin domain 3 (Tim-3);
An inhibitor of the V domain Ig inhibitor of e.T cell activation (Vista);
f.B and T lymphocyte attenuation factor (BTLA);
g. inhibitors of lymphocyte activation gene 3 (LAG 3); and
h.T cellular immunoglobulins and immunoreceptor tyrosine-based inhibitors of the inhibitory motif domain (TIGIT);
3) Telomerase inhibitors or telomeric DNA binding compounds;
4) Alkylating agents, including but not limited to: chlorambucil (leuken), oxaliplatin (ELOXATIN), streptozotocin (zanoar), dacarbazine, ifosfamide, lomustine (CCNU), procarbazine (MATULAN), temozolomide (temodiar), and thiotepa;
5) DNA cross-linking agents, including but not limited to: carmustine, chlorambucil (LEUKERAN), carboplatin (PARAPLATIN), cisplatin (PLATIN), busulfan (MYLERAN), melphalan (ALKERAN), mitomycin (MITOSOL), and cyclophosphamide (ENDOXAN);
6) Antimetabolites, including but not limited to: cladribine (LEUSTATIN), arabinoside (ARA-C), mercaptopurine (PURINETHOL), thioguanine, penstatin (NIPENT), cytosine arabinoside (cytarabine, ARA-C), gemcitabine (GEMZAR), fluorouracil (5-FU, CARAC), capecitabine (XELODA), folinic acid (FUSIEV), methotrexate (RHEMATREX), and raltitrexed;
7) Antimitotic agents, typically plant alkaloids and terpenes or derivatives thereof, include, but are not limited to: taxanes such as docetaxel (taxotere), paclitaxel (ABRAXANE, TAXOL), vinca alkaloids such as vincristine (onvin), vinblastine, vindesine, and vinorelbine (navlbine);
8) Topoisomerase inhibitors, including but not limited to: amsacrine, camptothecin (CTP), genistein (genistein), irinotecan (CAMPTOSAR), topotecan (HYCAMTIN), doxorubicin (ADRIAMYCIN), daunorubidine (CERUBIDINE), epirubicin (ELLENCE), ICRF-193, teniposide (VUMON), mitoxantrone (NOVANTRONE), and etoposide (epostin);
9) Inhibitors of DNA replication, including but not limited to: fludarabine (FLUDARA), afidomycin, ganciclovir and cidofovir;
10 Ribonucleoside diphosphate reductase inhibitors, including but not limited to: hydroxyurea;
11 Transcription inhibitors, including but not limited to: actinomycin D (dactinomycin, COSMEGEN) and plicamycin (mithramycin);
12 DNA cutting agents including, but not limited to: bleomycin (BLENOXANE) and idarubicin;
13 Aromatase inhibitors, including but not limited to: aminoglutethimide, anastrozole (arimid), letrozole (FEMARA), vorozole (RIVIZOR), and exemestane (aromiasin);
14 Angiogenesis inhibitors, including but not limited to: genistein, sunitinib (SUTENT) and bevacizumab (AVASTIN);
15 Anti-steroid or anti-androgen agents including, but not limited to: ammonia glutethimide (CYTADREN), bicalutamide (CASODEX), cyproterone, flutamide (EULEXIN), nilutamide (NILANDRON);
16 Tyrosine kinase inhibitors including, but not limited to: imatinib (GLEEVEC), erlotinib (TARCEVA), lapatinib (TYKERB), sorafenib (NEXAVAR), and acytinib (INLYTA);
17 mTOR inhibitors, including but not limited to: everolimus, temsirolimus (torsel) and sirolimus;
18 Apoptosis inducers such as cordycepin;
19 Protein synthesis inhibitors, including but not limited to: clindamycin, chloramphenicol, streptomycin, anisomycin, and cycloheximide;
20 Antidiabetic agents including, but not limited to: metformin and phenformin;
21 Cytotoxic antibiotics, including but not limited to:
a. tetracyclines, including but not limited to: doxycycline;
b. erythromycin classes, including but not limited to: azithromycin;
c. glycylglycines, including but not limited to: tigecycline;
d. antiparasitic agents, including but not limited to: pindolol (pyrvinium pamoate);
e. Beta-lactams including, but not limited to, penicillins and cephalosporins;
f. anthracyclines, including but not limited to: doxorubicin, daunorubicin, epirubicin, idarubicin, pirarubicin, aclarubicin and mitoxantrone;
g. bleomycins, such as classical bleomycin A2 (BLENOXANE) and pingyangmycin (also known as bleomycin A5)
h. Other antibiotics, including but not limited to: chloramphenicol, mitomycin C, and actinomycin D (dactinomycin, COSMEGEN); and
22 A) another agent, such as a BCG vaccine; buserelin (ETILAMIDE); chloroquine (ARALEN); clodronate, pamidronate or another bisphosphonate; colchicine; desmethylicin (demethoxyviridin); dichloroacetate; estramustine; feigiostin (neupgen); fludrocortisone (FLORINEF); goserelin (ZOLADEX); an interferon; folinic acid; leuprorelin (LUPRON); levamisole; lonidamine; mesna; metformin; mitotane (o, p' -DDD, LYSODREN); nocodazole; octreotide (SANDOSTATIN); pirifexin; porphil sodium (especially in combination with phototherapy and radiotherapy); suramin; tamoxifen; titanocene dichloride; tretinoin; anabolic steroids such as fluoxymestin (HALOTESTIN); estrogens such as estradiol, diethylstilbestrol (DES) and dienestrol; progestogens, such as medroxyprogesterone acetate (MPA) and megestrol; testosterone.
In some embodiments, drug moiety (D) may be a toxin. Plant-derived protein toxins include Ribosome Inactivating Proteins (RIP), such as shiga toxins type I (e.g., trichosanthin and luffin) and shiga toxins type II (e.g., ricin, lectin and abrin), as well as saporin, gelonin and pokeweed antiviral protein; and bacterial toxins include Pseudomonas exotoxin and diphtheria toxin.
In some embodiments, drug moiety (D) may be a diagnostic or detectable agent. Such immunoconjugates can be used to monitor or predict the onset, progression, progress and/or severity of a disease or disorder as part of a clinical test procedure, e.g., to determine the efficacy of a particular therapy. Such diagnosis and detection may be accomplished by coupling antibodies to detectable substances including, but not limited to, various enzymes such as horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; prosthetic groups such as, but not limited to, streptavidin and avidin/biotin; fluorescent materials such as, but not limited to, alexa Fluor 350, alexa Fluor 405, alexa Fluor 430, alexa Fluor 488, alexa Fluor500, alexa Fluor 514, alexa Fluor 532, alexa Fluor 546, alexa Fluor 555, alexa Fluor 568, alexa Fluor 594, alexa Fluor 610, alexa Fluor 633, alexa Fluor 647, alexa Fluor 660, alexa Fluor 680, alexa Fluor 700, alexa Fluor750, umbelliferone, fluorescein isothiocyanate, rhodamine, dichlorotriazinamine fluorescein, danyl chloride or Phycoerythrin; luminescent materials such as, but not limited to, luminol; bioluminescent materials such as, but not limited to, luciferase, luciferin and aequorin; radioactive substances, such as but not limited to iodine @, for example 131 I、 125 I、 123 I. And m i, C% 14 C) Sulfur 35 S), tritium and indium 115 In、 113 In、 112 In and m in, technetium ] 99 Tc), thallium 201 Ti, ga ] 68 Ga、 67 Ga and Pd% 103 Pd and molybdenum% 99 Mo and xenon 133 Xe and F 18 F)、 153 Sm、 177 Lu、 159 Gd、 149 Pm、 140 La、 175 Yb、 166 Ho、 90 Y、 47 Sc、 186 Re、 188 Re、 142 Pr、 105 Rh、 97 Ru、 68 Ge、 57 Co、 65 Zn、 85 Sr、 32 P、 153 Gd、 169 Yb、 51 Cr、 54 Mn、 75 Se、 64 Cu、 113 Sn and Sn 117 Sn; and positron-emitting metal and non-radioactive paramagnetic metal ions using various positron-emitting tomography.
In some embodiments, drug moiety D is selected from saporin, MMAE, MMAF, DM, DM4. In some embodiments, the drug is saporin.
Therapeutic application
Polypeptides (including antibodies and functional antigen binding fragments thereof), CAR-bearing immune effector cells, and compositions, antibody-drug conjugates, and pharmaceutical compositions comprising the same described herein, are useful for treating or preventing progression of proliferative diseases, such as cancer and myelodysplastic syndrome. The cancer may be a hematological malignancy or a solid tumor. Hematological malignancies include leukemia, lymphoma, multiple myeloma, and subtypes thereof. Lymphomas can be classified in various ways, typically based on the type of malignant cell that is potentially present, including hodgkin's lymphoma (typically cancer of the Reed-stent (Reed-stenberg) cell, but sometimes also of B-cell origin; all other lymphomas are non-hodgkin's lymphomas), non-hodgkin's lymphomas, B-cell lymphomas, T-cell lymphomas, mantle cell lymphomas, burkitt's lymphomas, follicular lymphomas, and other lymphomas as defined herein and known in the art. Myelodysplastic syndrome comprises a group of diseases affecting immature white blood cells and/or Hematopoietic Stem Cells (HSCs); MDS may develop into AML.
B-cell lymphomas include, but are not limited to diffuse large B-cell lymphomas (DLBCL), chronic Lymphocytic Leukemia (CLL)/Small Lymphocytic Lymphomas (SLL), and other B-cell lymphomas as defined herein and known in the art.
T cell lymphomas include T cell acute lymphoblastic leukemia/lymphoma (T-ALL), peripheral T Cell Lymphoma (PTCL), T cell chronic lymphocytic leukemia (T-CLL), sezary syndrome (Sezary syndrome), and other T cell lymphomas as defined herein and known in the art.
Leukemias include acute myeloid (or myelogenous) leukemia (AML), chronic myeloid (or myelogenous) leukemia (CML), acute lymphoblastic (or lymphoblastic) leukemia (ALL), chronic Lymphoblastic Leukemia (CLL), hairy cell leukemia (sometimes classified as lymphoma), and other leukemias as defined herein and known in the art.
Plasma cell malignancies include lymphoplasmacytic lymphomas, plasmacytomas, and multiple myelomas.
Solid tumors include melanoma, neuroblastoma, glioma, or carcinoma, such as tumors of the brain, head and neck, breast, lung (e.g., non-small cell lung cancer, NSCLC), genital tract (e.g., ovary), upper digestive tract, pancreas, liver, renal system (e.g., kidney), bladder, prostate, and colorectal.
The methods described herein are generally performed on a subject in need thereof. A subject in need of the therapeutic methods described herein can be a subject having, diagnosed with, suspected of having, or at risk of developing, or at risk of progressing to a later stage of cancer. The determination of treatment requirements will typically be assessed by medical history, physical examination, or diagnostic tests consistent with the disease or condition at issue. Diagnosis of various conditions treatable by the methods described herein is within the skill of the art. The subject may be an animal subject, including mammals, such as horses, cattle, dogs, cats, sheep, pigs, mice, rats, monkeys, hamsters, guinea pigs, and humans, or other animals, such as chickens. For example, the subject may be a human subject.
Generally, a safe and effective amount of a therapy (e.g., an antibody or functional antigen-binding fragment thereof, CAR-bearing immune effector cells, or antibody-drug conjugate) is an amount that will, for example, elicit a desired therapeutic effect in a subject while minimizing unwanted side effects.
According to the methods described herein, administration may be parenteral, pulmonary, oral, topical, intradermal, intramuscular, intraperitoneal, intravenous, intratumoral, intrathecal, intracranial, lateral intraventricular, subcutaneous, intranasal, epidural, ocular, buccal or rectal administration. For example, where the product is a biologic or cell therapy, the mode of administration will likely be via injection or infusion.
Standard of care and conditioning regimen for immunotherapy
Standard care treatments for cancer, such as AML, may involve anticancer drug therapies, including chemotherapy and targeted therapies, hematopoietic Stem Cell Transplantation (HSCT).
For example, the combination of cytarabine (cytosine arabinoside or ara-C) and an anthracycline such as daunorubicin (daunorubicin) or idarubicin is a first-line chemotherapy of AML. Other chemotherapeutic agents useful in the treatment of AML include cladribine (Leustatin, 2-CdA), fludarabine (Fludara), mitoxantrone, etoposide (VP-16), 6-thioguanine (6-TG), hydroxyurea, corticosteroids such as prednisone or dexamethasone, methotrexate (MTX), 6-mercaptopurine (6-MP), azacytidine (Vidaza), and decitabine (Dacog). In addition, targeted therapies may be used in appropriate patients, such as midostaurin (Rydapt) or gefitinib (xosapata) for patients with FLT-3 mutations; jituuzumab ozogamicin (gemtuzumab ozogamicin) (Mylotarg) for CD33 positive AML; BCL-2 inhibitors, e.g. vitamin EGram (Venclexta); IDH inhibitors such as Ai Funi buch (tibsosov) or exendipine (Idhifa); and hedgehog pathway inhibitors such as garagab (darisimo). Although the complete remission rate after initial induction chemotherapy can be as high as 80%, most AML patients will eventually progress to recurrent or refractory (RR) disease, and five-year survival of people under 60 years old is about 35%, and five-year survival of people over 60 years old is 10%. See Walter RB et al, "Resistance prediction in AML: analysis of 4601patients from MRC/NCRI, HOVON/SAKK, SWOG and MD Anderson Cancer Center [ prediction of resistance in AML: analysis of 4601patients from MRC/NCRI, HOVON/SAKK, SWOG and MD Andersen cancer center ]Leukemia [ Leukemia ]]29 (2) 312-20 (2015) andh et al, "Acute Myeloid Leukemia [ acute myeloid leukemia ]]"NEJM [ New England journal of medicine ]]373(12):1136-52(2015)。
Adoptive Cell Transfer (ACT) therapy may also treat cancer (e.g., AML) with or without conditioning regimens. Currently, hematopoietic Stem Cell Transplantation (HSCT) is used; other therapies such as transplantation of NK cells, chimeric Antigen Receptor (CAR) T cells (CAR-T) and other CAR-bearing immune effector cells are under development.
Hematopoietic Stem Cell Transplantation (HSCT)
Hematopoietic Stem Cell Transplantation (HSCT) is a potential curative treatment for a variety of malignant and non-malignant hematopoietic diseases such as AML, CML, ALL, hodgkin's lymphoma and non-hodgkin's lymphoma, multiple myeloma, myelodysplastic syndrome, neuroblastoma, ewing's sarcoma, glioma, and solid tumors. HSCT for AML is typically allogeneic and HLA matching between donor and patient is required for several reasons. First is the prevention of HvGD, but an additional benefit is graft versus leukemia (GvL) effect, where donor immune cells recognize patient leukemia cells as foreign and attack them. In some cases, for example, where the patient may not be tolerant of allografts, autografts may be used, typically after careful removal in an attempt to remove leukemia cells.
Typically, when HSCT is performed in a patient with a malignant disorder, a preparation regimen or conditioning regimen is administered as part of a procedure to achieve immune ablation to prevent graft rejection and reduce tumor burden. Traditionally, these objectives have been achieved by the use of superlethal doses of whole body irradiation (TBI) and chemotherapeutic agents with non-overlapping toxicity (so-called "high intensity" pre-HSCT conditioning) in other ways. However, since it is recognized that immune responses of donor cells against malignant host cells (i.e., graft anti-tumor effects) substantially contribute to the effectiveness of HSCT, conditioning protocols of reduced intensity and non-myeloablative have been developed, making HCT suitable for elderly and medically infirm patients.
Conditioning protocols are known in the art. See, e.g., gyurocza and Sandmaier BM, "Conditioning regimens for hematopoietic cell transplantation: one size does not fit all [ conditioning protocol for hematopoietic cell transplantation: one solution is not suitable for all people, "Blood [ Blood ]124 (3): 344-353 (2014). The conditioning regimen can be categorized as high dose (myeloablative), intensity-reduced, and non-myeloablative according to the intensity-reduced conditioning regimen conference held by the international blood and bone marrow transplant research Center (CIBMTR) during the 2006 bone marrow transplant tandem conference.
Immunotherapy using CAR-carrying immune effector cells
Immune effector cells carrying CARs have been used in the treatment of AML with varying results. Clinical trials using CAR-T cells targeting AML antigens (such as CD33 and CD 123) have been registered and are underway, but have not been definitely successful to date. One problem is that it is difficult to target the appropriate targetable surface antigens that are not expressed on healthy cells at the same time. CAR engineered cells from an immortalized NK-92 cell line targeting AML antigen CD33 were also tested.
In various contexts, therapies using CAR-carrying immune effector cells will be available for AML. In one scenario of treating an AML patient with CAR cell therapy, CARs present on the surface of immune effector cells carrying the CAR recognize and bind to AML cell antigens (such as CD33, FLT-3, or CLL-1), and AML cells are targeted for killing. CAR cell therapies will also target the same antigen on the patient's own hematopoietic stem cells. Thereafter, the patient receives Hematopoietic Stem Cell Transplantation (HSCT), optionally undergoing a preliminary procedure to destroy the CAR cells and precondition the patient for HSCT prior to the engrafted donor stem cells attacking the remaining AML cells. While this is an effective therapy for many patients, AML may still relapse (e.g., in about 50% of cases), and additional treatment with the same CAR cell therapy is typically not feasible because the implanted stem cells and their progeny would recognize the newly infused CAR stem cells as foreign and destroy them.
Polymorphic targeting of cancer antigens
Polymorphism targeting. Another approach to treating AML using CAR-bearing immune effector cells exploits the natural variation of AML target antigen polymorphisms to address this problem. Certain AML antigens (e.g., CD33, FLT-3, and CLL-1) appear as polymorphic variants. For example, in a given population, AML antigens exist as two major polymorphisms, e.g., a and B, in a given base pair in the genomic sequence of the antigen is a-T, in B the base pair at the same position is C-G. This will result in the translation of different amino acid residues and provided that base pairs are present in the coding region, resulting in antigens having different amino acid residues and thus different primary and thus tertiary structures. If the change is significant and the residues are in solvent exposed positions on the cell surface that are accessible to an antibody, antigen binding fragment thereof, or synthetic antigen binding protein (e.g., scFv), the CAR can be designed to selectively bind a single polymorphism relative to one or more other polymorphisms. And CAR-T cells or other immune effector cells carrying such selective CARs can target and kill AML cells in a single polymorphic form. See table 2 below, which lists three AML antigens and their common polymorphisms:
TABLE 2 polymorphism of AML antigens
Referring also to FIG. 1, the position of the extracellular domain of CD33 is shown, with amino acid 69 in the left panel and FLT3 ECD AA267 in the right panel each in a relatively solvent accessible position.
Patient-donor mismatch. Several useful therapeutic scenarios occur when a patient has one polymorphic form of AML antigen and a cell donor for HSCT has another polymorphic form of the antigen, thereby producing a "mismatch" of AML antigen polymorphisms.
When the donor provides polymorphic "mismatched" stem cells for HSCT, and those cells are implanted into the recipient patient, CAR-bearing immune effector cell therapy (with CARs selective for polymorphic variants of the patient) can be used to target and kill any remaining patient-bearing antigen polymorphic forms of cells, even after HSCT transplantation. Because these cells selectively target the patient's polymorphism, the donor's implanted cells will be retained. Treatment may be prophylactic or after the occurrence of signs of recurrent disease. Thus, recurrence is prevented or treated, and the patient can achieve disease-free survival.
HSCs and T cells or other immune effector cells to be engineered to express a CAR may both be from the same donor, which is polymorphic mismatched to the intended recipient. As shown in table 3 below, the donor must be homozygous (i.e., not heterozygous) for one polymorphism or the other, and the recipient patient may be homozygous or heterozygous for the other.
TABLE 3 therapeutic regimens for anti-CD 33 polymorphic antibodies and CARs
In another variation, the HSCs can be from one mismatched donor, and the immune effector cells that will be engineered to express the CAR will be from a different donor. If the CAR-bearing immune effector cells are CAR-T cells, these cells may disable T cell receptors, for example, by gene disruption of one or more components thereof (e.g., TRAC) using, for example, CRISPR or another genome editing tool or technique (e.g., PEBL).
Pharmaceutical composition
Also disclosed are pharmaceutical compositions comprising the disclosed molecules in a pharmaceutically acceptable carrier. Pharmaceutical carriers are known to those skilled in the art. These will most typically be standard carriers for administering drugs to humans, including solutions such as sterile water, saline, and physiological pH buffered solutions. Typically, an appropriate amount of a pharmaceutically acceptable salt is used in a formulation to impart isotonicity to the formulation. Examples of pharmaceutically acceptable carriers include, but are not limited to, saline, ringer's solution, and dextrose solution. The pH of the solution is preferably from about 5 to about 8, and more preferably from about 7 to about 7.5. The solution should be free of RNase. Additional carriers include sustained release formulations such as semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, liposomes, or microparticles. It will be apparent to those skilled in the art that certain carriers may be more preferred, depending on, for example, the route of administration and the concentration of the composition being administered.
In addition to the selected molecules, the pharmaceutical compositions may also include carriers, thickeners, diluents, buffers, preservatives, surfactants and the like. The pharmaceutical composition may also include one or more active ingredients, such as antimicrobial agents, anti-inflammatory agents, anesthetics, and the like.
Formulations for parenteral administration include sterile aqueous or nonaqueous solutions, suspensions and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils (such as olive oil) and injectable organic esters (such as ethyl oleate). Aqueous carriers include water, alcohol/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, ringer's dextrose, dextrose and sodium chloride, lactated ringer's solution, or fixed oils. Intravenous vehicles include fluid and nutritional supplements, electrolyte supplements (such as those based on ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, antioxidants, chelating agents, and inert gases and the like.
Definition of the definition
Unless defined otherwise, technical and scientific terms used in connection with this disclosure should have the meaning commonly understood by one of ordinary skill in the art. Furthermore, unless the context requires otherwise, singular terms shall include the plural and plural terms shall include the singular. In general, the nomenclature used in connection with the cell and tissue culture, molecular biology, and protein and oligomer or polynucleotide chemistry and hybridization described herein, and the techniques thereof, are those well known and commonly employed in the art.
The terms "polypeptide", "peptide" and "protein" are used interchangeably herein to refer to a polymer of amino acid residues. These terms also apply to amino acid polymers in which one or more amino acid residues are artificial chemical mimics of the corresponding naturally occurring amino acid, and to naturally occurring amino acid polymers as well as non-naturally occurring amino acid polymers.
As used herein, the term "antibody" is meant to include classical immunoglobulin sequence elements (sufficient to confer specific binding or, for example, an immune response) and/or polypeptides directed against a particular target antigen. As known in the art, naturally occurring intact antibodies are approximately 150kD tetrameric reagents, which consist of two identical heavy chain polypeptides (approximately 50kD each) and two identical light chain polypeptides (approximately 25kD each) associated with each other into what is commonly referred to as a "Y-shaped" structure. Each heavy chain consists of at least four domains (each about 110 amino acids in length): amino terminal variable (V H ) The domain is followed by three constant domains: c (C) H 1、C H 2. C at the carboxyl terminus H 3. The short region, called the "switch", connects the heavy chain variable and constant regions. "hinge" will C H 2 and C H The 3 domain is linked to the rest of the antibody. The two disulfide bonds of the hinge region link the two heavy chain polypeptides in the intact antibody to each other. Each light chain consists of two domains: amino terminal variable (V L ) Domain followed by carboxy-terminal constant (C L ) Domains, which are separated from each other by another "switch". The complete antibody tetramer is composed of two heavy chainsA light chain dimer, wherein the heavy and light chains are linked to each other by a single disulfide bond; the other two disulfide bonds connect the heavy chain hinge regions to each other, allowing the dimers to connect to each other and form a tetramer. Naturally occurring antibodies are also glycosylated, typically at C H 2 domain. The structure of each domain in a natural antibody is characterized by an "immunoglobulin fold" formed by two beta sheets (e.g., 3-, 4-, or 5-chain sheets) that are packaged relative to each other in a compressed antiparallel beta barrel. Each variable domain contains three hypervariable loops called "complementarity determining regions" (CDR 1, CDR2, and CDR 3) and four slightly unchanged "framework" regions (FR 1, FR2, FR3, and FR 4). When the natural antibody is folded, the FR regions form beta sheets that provide structural framework for the domains, and the CDR loop regions from the heavy and light chains are clustered together in three dimensions such that they create a single hypervariable antigen binding site at the tip of the Y structure. The Fc region of naturally occurring antibodies binds to elements of the complement system and also to receptors on effector cells, including, for example, effector cells that mediate cytotoxicity.
The term "antigen" refers to a molecular entity that may be soluble or specifically cell membrane-bound, but is not limited to a molecular entity that is recognizable by the adaptive immune system, including but not limited to an antibody or TCR, or an engineered molecule including but not limited to a transgenic TCR, chimeric Antigen Receptor (CAR), scFv or multimer thereof, fab fragment or multimer thereof, antibody or multimer thereof, single chain antibody or multimer thereof, or any other molecule capable of achieving binding to a structure with high affinity.
With respect to antigen recognizing receptors, the term "specifically binds" or "has specificity for … …" or "specifically recognizes" refers to the antigen binding domain of the antigen recognizing receptor that recognizes and binds a specific polymorphic variant of an antigen, but does not substantially recognize or bind other variants.
The term "monoclonal antibody" (mAb) as applied to antibodies described in this disclosure is a compound derived from a single copy or clone of any eukaryotic, prokaryotic, or phage clone, and not a method of its production. The mabs of the present disclosure may be present in homogeneous or substantially homogeneous populations.
As used herein, the term "binding affinity" refers to the strength of a molecule to bind to another molecule at a site on the molecule. If a particular molecule is to bind to or specifically associate with another particular molecule, then the two molecules are said to exhibit binding affinity for each other. Binding affinity is related to the association and dissociation constants of a pair of molecules, but these constants are not critical to the methods herein, measured or determined separately. In contrast, affinity as used herein to describe interactions between molecules of these described methods is typically the apparent affinity observed in empirical studies (unless otherwise indicated) that can be used to compare the relative strength with which one molecule (e.g., an antibody or other specific binding partner) will bind to two other molecules (e.g., two forms or variants of a peptide). The concepts of binding affinity, association constant, and dissociation constant are well known.
As used herein, the term "sequence identity" means the percentage of identical nucleotides or amino acid residues at corresponding positions in two or more sequences when the sequences are aligned to maximize sequence matching (i.e., taking into account gaps and insertions). Identity can be easily calculated by known methods. The method for determining identity is designed to give the greatest match between the sequences tested. Furthermore, methods of determining identity are compiled in publicly available computer programs. For example, optimal sequence alignment for comparison can be performed by the local homology algorithm of Smith and Waterman, by the homology alignment algorithm, by the similarity search method, or by computerized execution of these algorithms (GAP, BESTFIT, PASTA and TFASTA in the GCG Wisconsin software package (Wisconsin Package), available from the company Anson Nix (Accelrys, inc.). Often see Altschul, S.F. et al, J.mol.biol. [ J. Mol. Biol. ]215:403-410 (1990) and Altschul et al Nucl. Acids Res. [ nucleic acids research ]25:3389-3402 (1997)). One example of an algorithm suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm.
An "antibody fragment" refers to a molecule that is not an intact antibody, comprising a portion of an intact antibody that binds to an antigen to which the intact antibody binds. Several examples of antibody fragments include, but are not limited to Fv, fab, fab ', fab ' -SH, F (ab ') 2 Diabodies, linear antibodies, single chain variable fragments (scFv), and multispecific antibodies formed from antibody fragments. In some embodiments, the antibody fragment is an antigen binding fragment.
A review of current methods for antibody engineering and improvement can be found in R.Kontermann and S.Dubel, (2010)Antibody Engineering[ antibody engineering ]]Roll 1 and roll 2Springer Protocols [ Schepringer protocol ]]Version 2 and w.strohl and l.strohl (2012)Therapeutic antibody engineeringCurrent and future advances driving the strongest growth area in the pharmaceutical industry [ therapeutic antibody engineering: current and future developments driving the strongest growth area in the pharmaceutical industry]Woodhead Publishing [ Wu Dehai De Press ]]. Methods for producing and purifying antibodies and antigen binding fragments are well known in the art and can be found in Harlow and Lane (1988)Antibodies:A LaboratoryManual[ antibody: laboratory manual]Cold Spring Harbor Laboratory Press Cold spring harbor laboratory Press ]Cold spring harbor, new York, chapters 5-8 and 15.
By "diseased cell" is meant a cell, tissue or organism whose state differs from normal or healthy and which may be caused by the effects of pathogens, toxic substances, irradiation or cell internal disorders. "diseased cells" may also refer to cells that have been infected with a pathogenic virus. Furthermore, the term "diseased cell" may refer to a malignant cell or a neoplastic cell that may constitute or cause cancer in an individual.
The term "cancer" is medically known as malignant neoplasm. Cancer is a broad group of diseases involving up-regulation of cell growth. In cancer, cells (cancerous cells) divide and grow uncontrollably, forming malignant tumors, and invade nearby body parts. Cancer may also spread to more distant sites in the body through the lymphatic system or blood flow. More than 200 different cancers affecting humans are known.
The term "malignancy" or "malignancy" describes a cell, population of cells or tissue that makes up a neoplasm, which originates from the neoplasm or may be the source of new neoplastic cells. The term is used to describe neoplastic cells in contrast to normal or healthy cells of tissue. Malignant tumors are compared to non-cancerous benign tumors in that the growth of the malignant tumor is not self-limiting, can invade adjacent tissues, and may be able to spread to distant tissues. Benign tumors do not have these properties. Malignant tumors are characterized by meta-changes, invasiveness and metastasis, and genomic instability. The term "precancerous cell" refers to a cell or tissue that is not yet malignant but is about to become malignant.
The term "chemotherapy" refers to the treatment of cancer (cancerous cells) using one or more cytotoxic anti-neoplastic agents ("chemotherapeutic agents" or "chemotherapeutic agents") as part of a standardized regimen. Administration of chemotherapy may have a curative intent, or it may be intended to extend longevity or alleviate symptoms. It is often used in combination with other cancer treatments such as radiation therapy, surgery and/or hyperthermia. Traditional chemotherapeutic agents act by killing rapidly dividing cells, one of the main characteristics of most cancer cells. This means that chemotherapy also damages cells that divide rapidly under normal conditions, such as cells in the bone marrow, digestive tract, and hair follicles. This results in the most common side effects of chemotherapy, such as myelosuppression (reducing blood cell production and thus also immunosuppression), mucositis (inflammation of the lining of the digestive tract) and hair loss (hair loss).
The term "immune cell" or "immune effector cell" refers to a cell that may be part of the immune system and performs a specific effector function, such as an alpha-beta T cell, NK cell (including ML-NK and CIML-NK), NKT cell (including iNKT cell), B cell, innate Lymphocyte (ILC), cytokine-induced killer (CIK) cell, lymphokine-activated killer (LAK) cell, gamma-delta T cell, mesenchymal stem cell or Mesenchymal Stromal Cell (MSC), monocyte and macrophage. Preferred immune cells are cells having cytotoxic effector functions, such as alpha-beta T cells, NK cells (including ML-NK and CIML-NK), NKT cells (including inKT cells), ILC, CIK cells, LAK cells or gamma-delta T cells. "effector function" means a specific function of a cell, for example in a T cell, and the effector function may be cytolytic activity or helper activity, including secretion of cytokines.
The term "side effect" refers to any complication, unwanted or pathological outcome of immunotherapy using antigen recognizing receptors, in addition to the desired therapeutic outcome. The term "side effect" preferably refers to off-target tumor toxicity that may occur during immunotherapy in the presence of a target antigen on a cell that is a non-target cell expressing the antigen, but not a diseased cell as described herein. A side effect of immunotherapy may be the development of graft versus host disease.
The term "reducing side effects" refers to reducing the severity of any complications, unwanted or pathological consequences of immunotherapy using antigen recognizing receptors, such as toxicity to non-target cells expressing the antigen. "reducing side effects" also refers to measures that reduce or avoid the risk of pain, injury or death of a patient during immunotherapy using antigen recognizing receptors.
The term "combination immunotherapy" refers to the co-application of two therapeutic methods, such as those known in the art for the treatment of diseases such as cancer. The term "combination immunotherapy" may also refer to the co-application of an immunotherapy (e.g. treatment with antigen recognizing receptors) and another therapy, such as the transplantation of hematopoietic cells (e.g. hematopoietic cells that are resistant to recognition of antigen recognizing receptors). Expression of an antigen on a cell means that the antigen is sufficiently present on the cell surface of the cell that it can be detected, bound and/or recognized by an antigen recognizing receptor.
The term "hematopoietic cells" refers to a population of cells of the hematopoietic lineage capable of hematopoietic formation, including but not limited to hematopoietic stem cells and/or hematopoietic progenitor cells (i.e., capable of proliferating and at least partially reconstituting different blood cell types, including erythroid cells, lymphocytes, and bone marrow cells). As used herein, the term "hematopoietic cells" also includes cells that differentiate from hematopoietic stem cells and/or hematopoietic progenitor cells to form blood cells (i.e., blood cell types, including erythroid cells, lymphocytes, and bone marrow cells).
By donor hematopoietic cells that are resistant to antigen recognition receptor recognition antigens is meant that the cells cannot be detected, bound and/or recognized as readily by or are impaired by antigen recognition receptors specific for the antigen, and therefore the cells are not killed during immunotherapy.
The term "self-phase killing" refers to the observation that in addition to diseased cells, antigens associated with disease may also be present on engineered immune effector cells, such as T cells expressing antigen recognizing receptors (e.g., CARs). In this case, the side effects of the antigen recognizing receptor will affect immune effector cells engineered to express the antigen recognizing receptor. Such side effects are also known in the art as autogenous killing.
In general, the term "receptor" refers to a biological molecule that may be soluble or attached to a cell surface membrane and specifically binds to a defined structure that may be attached to the cell surface membrane or soluble. Receptors include, but are not limited to, antibodies and antibody-like structures, adhesion molecules, transgenic or naturally occurring TCRs or CARs. In particular, as used herein, the term "antigen recognizing receptor" may be a membrane-bound receptor or a soluble receptor, such as a native TCR, transgenic TCR, CAR, scFv or multimer thereof, fab fragment or multimer thereof, antibody or multimer thereof, bispecific T cell enhancer (BiTE), diabody or any other molecule capable of achieving specific binding with high affinity.
The term "target" or "target antigen" refers to any cell surface protein, glycoprotein, glycolipid, or any other structure present on the surface of a target cell. The term also refers to any other structure that is specifically present on the target cell, but is not limited to a structure that is recognizable by an adaptive immune system including, but not limited to, an antibody or TCR, or an engineered molecule including, but not limited to, a transgenic TCR, CAR, scFv or multimer thereof, a Fab fragment or multimer thereof, an antibody or multimer thereof, a single chain antibody or multimer thereof, or any other molecule capable of achieving binding to a structure with high affinity.
As used herein, the term "target cell" refers to a cell that is recognized by an antigen recognizing receptor applied or to be applied to an individual.
As used herein, the term "system for immunotherapy" refers to a collection of two compositions that are required to perform a combination immunotherapy as disclosed herein. Thus, the system (or kit or combination of compositions) comprises a) an antigen recognizing receptor, wherein the antigen recognizing receptor specifically recognizes an antigen on a target cell in the individual; b) Hematopoietic cells that are resistant to recognition of the antigen by the antigen recognizing receptor.
"chimeric antigen receptor" or "CAR" refers to an engineered receptor that specifically grafts an antigen to a cell (e.g., a T cell). The CARs disclosed herein comprise an antigen binding domain (also referred to as an antigen targeting region), an extracellular spacer domain or hinge region, a transmembrane domain, and at least one intracellular signaling domain or at least one co-stimulatory domain and at least one intracellular signaling domain.
In general, a CAR can comprise an extracellular domain (extracellular portion), a transmembrane domain, and an intracellular signaling domain that comprises an antigen binding domain. The extracellular domain may be linked to the transmembrane domain by a linker. The extracellular domain may also comprise a signal peptide.
"Signal peptide" refers to a peptide sequence that directs the transport and localization of a protein within a cell, for example, to a certain organelle (e.g., the endoplasmic reticulum) and/or cell surface.
An "antigen binding domain" refers to a region in a CAR that specifically binds to an antigen (and is thus capable of targeting an antigen-containing cell). The CAR may comprise one or more antigen binding domains. Typically, the targeted region on the CAR is extracellular. The antigen binding domain may comprise an antibody or antigen binding fragment thereof. The antigen binding domain may comprise, for example, a full length heavy chain, a Fab fragment, a single chain Fv (scFv) fragment, a bivalent single chain antibody, or a diabody. Any molecule that specifically binds to a given antigen (e.g., an affibody or ligand binding domain from a naturally occurring receptor) can be used as the antigen binding structureDomain. The antigen binding domain is typically a scFv. Normally, in scFv, the variable parts of the immunoglobulin heavy and light chains are fused by a flexible linker to form the scFv. Such a linker may be, for example (GGGGGG) 4 S) 3 . In some cases, it is beneficial that the antigen binding domain is derived from the same species in which the CAR is to be used. For example, when the CAR is intended to be used therapeutically in a human, it may be beneficial for the antigen binding domain of the CAR to comprise a human or humanized antibody or antigen binding fragment thereof. The human or humanized antibodies or fragments thereof may be prepared by a variety of methods well known in the art.
As used herein, "spacer" or "hinge" refers to a hydrophilic region between an antigen binding domain and a transmembrane domain. The CARs disclosed herein may comprise an extracellular spacer domain, but such spacers may also be skipped. The spacer may comprise an Fc fragment of an antibody or fragment thereof, a hinge region of an antibody or fragment thereof, a CH2 or CH3 region of an antibody, a helper protein, an artificial spacer sequence, or a combination thereof. A prominent example of a spacer is a CD8 a hinge.
The "transmembrane domain" of a CAR may be derived from any desired natural or synthetic source of such domain. When the source is natural, the domain may be derived from any membrane-bound protein or transmembrane protein. The transmembrane domain may be derived from, for example, CD8 a or CD28. When the key signaling and antigen recognition modules are on two (or even more) polypeptides, then the CAR may have two (or more) transmembrane domains. Because of the small molecule-dependent heterodimerization domain in each polypeptide of the CAR, splitting the key signaling and antigen recognition modules enables small molecule-dependent, titratable, and reversible control of CAR cell expression (Wu et al 2015, science [ science ] 350:293-303).
The cytoplasmic domain or intracellular signaling domain of the CAR is responsible for activating at least one normal effector function of the immune cell expressing the CAR. "effector function" means a specific function of a cell, for example in a T cell, and the effector function may be cytolytic activity or helper activity, including secretion of cytokines. Intracellular signaling domain refers to the portion of the protein that transduces effector function signals and directs CAR-expressing cells to perform a particular function.
The intracellular signaling domain may comprise any complete or truncated portion of the intracellular signaling domain of a given protein sufficient to transduce an effector function signal. Prominent examples of intracellular signaling domains for CARs include cytoplasmic sequences of T Cell Receptors (TCRs) and co-receptors that work together to initiate signal transduction upon antigen receptor engagement.
In general, T cell activation can be mediated by two different classes of cytoplasmic signaling sequences, firstly those that initiate antigen dependent primary activation by a TCR (primary cytoplasmic signaling sequences), and secondly those that act in an antigen independent manner to provide secondary or costimulatory signals (secondary cytoplasmic signaling sequences, costimulatory signaling domains). Thus, the intracellular signaling domain of the CAR may comprise a primary cytoplasmic signaling domain and/or a secondary cytoplasmic signaling domain.
The primary cytoplasmic signaling sequence that acts in a stimulatory manner may contain ITAM (immune receptor tyrosine based activation motif signaling motif). Examples of ITAM-containing primary cytoplasmic signaling sequences frequently used in CARs are those derived from TCR ζ (cd3ζ), fcrγ, fcrβ, cd3γ, cd3δ, cd3ε, CD5, CD22, CD79a, CD79b, and CD66 d. Most prominent is the sequence derived from cd3ζ.
The cytoplasmic domain of the CAR may be designed to comprise the CD 3-zeta signaling domain itself, or a combination thereof with any other desired cytoplasmic domain or domains. The cytoplasmic domain of the CAR can comprise a cd3ζ chain portion and a costimulatory signaling region. A costimulatory signaling region refers to the portion of the CAR that comprises the intracellular domain of a costimulatory molecule. Costimulatory molecules are cell surface molecules other than antigen receptors or their ligands that are required for the efficient response of lymphocytes to antigens. Examples of costimulatory molecules are CD27, CD28, 4-1BB (CD 137), OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3. Cytoplasmic signaling sequences within the cytoplasmic signaling portion of the CAR can be linked to each other in random or specific order. Preferably a short oligopeptide or polypeptide linker of 2 to 10 amino acids in length may form the connection. The protruding linker is a glycine-serine duplex.
By way of example, the cytoplasmic domain may comprise the signaling domain of CD 3-zeta and the signaling domain of CD 28. In another example, the cytoplasmic domain can comprise a signaling domain of CD3- ζ and a signaling domain of CD 27. In further examples, the cytoplasmic domain can comprise a signaling domain of CD3- ζ, a signaling domain of CD28, and a signaling domain of CD 27.
As previously mentioned, the extracellular portion or transmembrane domain or cytoplasmic domain of the CAR may also comprise a heterodimerization domain in order to split the key signaling and antigen recognition modules of the CAR.
The CAR can be designed to comprise any combination of any portion (part or portion) of the domains described above as described herein to produce a functional CAR.
A "chimeric antigen receptor" has at least one antigen-specific variable region (typically a single chain variable region consisting of antibody heavy and light chain variable regions) linked to an effector cell signaling domain of: typically, the intracellular domain of a T cell receptor, exemplified by (but not limited to) the zeta domain of CD 3. Upon binding of the antigen-specific region to the corresponding antigen, the signaling domain mediates effector cell function (e.g., cytotoxicity) in the host cell. The CAR may optionally, but not necessarily, comprise additional domains, such as linkers, transmembrane domains, and other intracellular signaling elements as described above.
The term "genetically modified" or "genetically modified" refers to a change in the content of a nucleic acid (including, but not limited to, genomic DNA of a cell). This includes, but is not limited to, altering the genomic DNA sequence of a cell by introducing, exchanging or deleting individual nucleotides or fragments of the nucleic acid sequence. The term also refers to any introduction of nucleic acid into a cell, regardless of whether it results in a direct or indirect change in the genomic DNA sequence of the cell.
As used herein, the terms "engineered cell" and "genetically modified cell" may be used interchangeably. The term means that the foreign gene or nucleic acid sequence is contained and/or expressed, which in turn modifies the genotype or phenotype of the cell or its offspring. These terms refer in particular to the fact that cells can be manipulated by recombinant methods well known in the art to express peptides or proteins stably or transiently, which are not expressed in these cells in their natural state. Genetic modification of a cell may include, but is not limited to, transfection, electroporation, nuclear transfection, transduction using retroviral vectors, lentiviral vectors, non-integrated retroviruses or lentiviral vectors, transposons, design nucleases (including zinc finger nucleases, TALENs or CRISPR/Cas).
The term "therapeutically effective amount" means an amount that provides a therapeutic benefit.
Immunotherapy is a medical term defined as "treating a disease by inducing, enhancing, or suppressing an immune response. Immunotherapy designed to elicit or amplify an immune response is classified as an activated immunotherapy, while immunotherapy rules that reduce or suppress an immune response are classified as a suppressed immunotherapy. Cancer immunotherapy, which is an activated immunotherapy, attempts to stimulate the immune system to repel and destroy tumors. Adoptive cell transfer uses a cell-based cytotoxic response to attack cancer cells. Immune cells (e.g., T cells) that are naturally or genetically engineered reactive to the patient's cancer are generated in vitro and then transferred back into the cancer patient.
As used herein, the term "transplantation" means the administration of a donor cell population, such as hematopoietic cells or CAR-bearing immune effector cells, to a subject.
As used herein, the term "treating" means reducing the frequency or severity of at least one sign or symptom of a disease.
As used herein, the term "individual" refers to an animal. Preferably, the subject is a mammal, such as a mouse, rat, cow, pig, goat, chicken, dog, monkey, or human. More preferably, the individual is a human. The individual may be an individual (patient) suffering from a disease, such as cancer, but the subject may also be a healthy subject.
As used herein, the term "fold-selectivity" means that the affinity for one target (e.g., a first polymorphic variant of an antigen) is at least x-fold greater than its affinity for another target (e.g., a second polymorphic variant of an antigen), where x is at least 2 and may be higher, such as 10, 20, 50, 100, or 1000. In a preferred embodiment, fold selectivity is therapeutically significant, i.e., sufficient to allow killing of cells expressing one target and killing of cells carrying the other target.
Examples
Example 1: identification of targets for polymorphic selective polypeptides
Polymorphic selective polypeptides for antigen targets can be identified, optimally, these targets 1) have targetable moieties in the extracellular domain, 2) are solvent exposed and accessible for binding of polymorphic selective polypeptides (e.g., scFv), 3) have high population frequencies such that donor-patient mismatches are possible, and 4) have high antigen densities on target cells.
For example, CD33 ARG69GLY has a high population frequency with a Minimum Allele Frequency (MAF) of 0.42. Similarly, the MAF of CLL-1LYS244GLN is 0.35 and the MAF of FLT3 THR227MET is 0.40.
Example 2: identification of anti-human CD33 scFv clones
Two recombinant polymorphic forms of human CD33 extracellular domain antigen (CD 33 R69 And CD33 G69 ) Selective anti-human CD33 scFv clones were found by standard screening methods for human antibody libraries. A variety of panning strategies are employed to facilitate enrichment of thermostable clones with the desired range of affinities. scFv were screened for selective binding between two Single Nucleotide Polymorphism (SNP) variants of human CD33 (arginine 69 and glycine 69) by flow cytometry and Biological Layer Interferometry (BLI), for example as described below in examples 5 and 6. The selected sequences are disclosed in the following polypeptides 1-42.
Additional anti-human CD33 polypeptides can be identified using these methods.
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Example 3: identification of anti-human CLL-1scFv clones
A method similar to that in example 1 has been used to find selective anti-human CLL-1scFv clones. Selective anti-human CLL-1scFv clones were found by standard screening methods of human antibody libraries using two recombinant polymorphic forms of human CLL-1 extracellular domain antigen (CLL-1-K244 and CLL-1-Q244). Using these antigens, a variety of panning strategies are employed to facilitate enrichment of thermostable clones with the desired range of affinities. scFv were screened for selective binding between two Single Nucleotide Polymorphism (SNP) variants of human CLL-1 (lysine 244 and glutamine 244) by Biological Layer Interferometry (BLI).
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Example 4: flow cytometry (FACS)
For CD33, jurkat cells were engineered to stably express huCD33-R69 or huCD33-G69 variants at >200,000 receptors per cell. The parental huCD33-R69 and huCD33-G69 Jurkat cell lines were stained with different levels of CellTrace violet cell proliferation kit (ThermoFisher, cat. No. C34557) to barcode each cell line. The bar-coded Jurkat cell line was fixed with paraformaldehyde and incubated with myc-tagged scFv periplasmic extract and secondary anti-myc PE conjugated monoclonal antibody. Appropriate positive and negative controls were used. Stained cells were analyzed by flow cytometry (CytoFLEX, beckman Coulter, inc.) and binding was assessed by changes in PE Mean Fluorescence Intensity (MFI) of barcode encoded cell populations.
For FLT3, ramos cells were engineered to stably express huFLT3-T227 or huFLT3-M227 variants at >200,000 receptors per cell. Parental huFLT3-T227 and huFLT3-M227 Ramos cell lines were stained with different levels of CellTrace violet cell proliferation kit (sameimer femto, cat# C34557) to barcode each cell line. Bar coded Ramos cell lines were fixed with paraformaldehyde and incubated with myc-tagged scFv periplasmic extracts and secondary anti-myc PE conjugated monoclonal antibodies. Appropriate positive and negative controls were used. Stained cells were analyzed by flow cytometry (CytoFLEX, beckmann coulter, inc.) and binding was assessed by changes in PE Mean Fluorescence Intensity (MFI) of bar-coded cell populations.
For CD33, the results of this assay are shown in table 8a, which reports the fold change relative to the parent as (-): indication < 2-fold; (+): indicating 2-10 times; (++): indicating 10-30 times; and [ (II) a ] ++ +): indicated >30 times. The data are also shown in fig. 2 and 3.
TABLE 8a polypeptide Selectivity-CD 33
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The foregoing method may be applied to demonstrate binding and polymorphic selectivity of other scfvs to antigens such as cancer antigens. For example, these methods are expected to demonstrate that anti-FLT 3 scFv selectively binds to the T227 or T227M polymorphism.
Example 5: biological Layer Interferometry (BLI)
Binding of scFv found using BLI analysis to huCD33-R69-His or huCD33-G69-Fc recombinant proteins (for anti-CD 33 scFv, for CLL-1scFv, huCLL1-K244-Avi-Tev-His or huCLL1-Q244-Avi-Tev-His, for FLT3, huFLT3-T227-His or huFLT 3-M227-Fc) was performed on an Octet HTX instrument from Bolborodi BioCo (ForteBio). Streptavidin-coated biosensors were loaded with biotinylated anti-V5 tag monoclonal antibody for 5min, then quenched with 20 μm amine-PEG 2-biotin and blocked for 5min. Scfvs from periplasmic extracts of scFv clones were captured on a biosensor. The huCD33 (or huCLL-1, or huFLT 3) proteins were then associated with the captured scFv for 2 minutes followed by dissociation with buffer (1X HBST[10mM HEPES pH 7.4, 150mM NaCl,0.05%Tween-20],1g/L BSA) for 5 minutes. Data for the reference buffer was subtracted against the negative control scFv and report spots were collected at time points (115 seconds or 119 seconds) immediately before the end of the association step to assess yes/no binding. The data were fitted with a 1:1 langmuir equation (Langmuir equation) and the values of the dissociation rates reported.
For CD33, the results of this assay are shown in table 9a, which reports binding, non-binding or ambiguities.
TABLE 9A polypeptide Selectivity-CD 33
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Similar methods were used to assess the selectivity of binding of polypeptides to CLL-1K244 or CLL-1Q 244. The results of this assay are shown in table 9b, which reports binding, non-binding or ambiguities.
TABLE 9b polypeptide Selectivity-CLL-1
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Example 6: chimeric antigen receptor comprising scFv
Examples of chimeric antigen receptors comprising scFv as disclosed herein are provided below in tables 10 and 11, which can be constructed and expressed in immune effector cells according to methods known in the art and disclosed herein (CAR examples 1-60). Tables 10 and 11 are intended to provide how V comprising scFv disclosed herein can be constructed H And V L Examples of chain CARs. Additional CARs can be derived from other scFv V disclosed herein H And V L Chain construction.
The CAR in table 10 below has the form:
i- - [ (Signal) (scFv V H ) (linker) (scFv V L ) (hinge) (TMD) (Co-stimulus) (effector)]- |++ (tag)
Or alternatively
I- - [ (Signal) (scFv V L ) (linker) (scFv V H ) (hinge) (TMD) (Co-stimulus) (effector)]- |++ (tag),
wherein:
CD8a signal sequence MALPVTALLLPLALLLHAARP has SEQ ID NO:1521, or alternatively, one of SEQ ID NO.1522-1525 may be used;
·(GGGGS) 4 The linker has SEQ ID NO. 1536, or alternatively, one of SEQ ID NO.1532-1535 may be used;
CD8 hinge sequence TTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTR
GLDFACD has SEQ ID NO:1526;
CD28 transmembrane domain sequence FWVLVVVGGVLACYSLLVTVAFIIFWV has SEQ ID NO:1527;
CD28 costimulatory domain sequence RSKRSRLLHSDYMNMTPRRPGPTRKHYQPYAP PRDFAAYRS has the sequence of SEQ ID NO 1530;
4-1BB costimulatory domain sequence KRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRF PEEEEGGCEL has the sequence of SEQ ID NO:1529;
CD3z effector domain sequence RVKFSRSADAPAYKQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPRRKNPQEGLYNELQKDKMAEAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR has SEQ ID NO. 1531;
P2A sequence GSGATNFSLLKQAGDVEENPGP has SEQ ID NO. 1532;
CD34 tag sequence MPRGWTALCLLSLLPSGFMSLDNNGTATPELPTQGTFSNVSTNVSYQETTTPSTLGSTSLHPVSQHGNEATTNITETTVKFTSTSVITSVYGNTNSSVQSQTSVISTVFTTPANVSTPETTLKPSLSPGNVSDLSTTSTSLATSPTKPYTSSSPILSDIKAEIKCSGIREVKLTQGICLEQNKTSSCAEFKKDRGEGLARVLCGEEQADADAGAQVCSLLLAQSEVRPQCLLLVLANRTEISSKLQLMKKHQSDLKKLGILDFTEQDVASHQSYSQKTLIALVTSGALLAVLGITGYFLMNRRSWSPI has SEQ ID NO 1537, or alternatively, a variant or truncated CD34 sequence may be used;
V of examples 1-3 and 31-33 H And V L The domains are from polypeptide 1, e.g., from SEQ ID NO 151 and SEQ ID NO 176, respectively;
v of examples 4-6 and 34-36 H And V L The domains are from polypeptide 5, e.g., from SEQ ID NO 155 and SEQ ID NO 180, respectively;
v of examples 7-9 and 37-39 H And V L The domains are from polypeptide 6, e.g., from SEQ ID NO 156 and SEQ ID NO 181, respectively;
v of examples 10-12 and 40-42 H And V L The domains are from polypeptide 7, e.g., from SEQ ID NO. 157 and SEQ ID NO. 182, respectively;
v of examples 13-15 and 43-45 H And V L The domains are from polypeptide 25, e.g., from SEQ ID NO 175 and SEQ ID NO 200, respectively;
v of examples 16-18 and 46-48 H And V L The domain is derived from the polypeptide 30,for example from SEQ ID NO 307 and SEQ ID NO 324, respectively;
v of examples 19-21 and 49-51 H And V L The domains are from polypeptide 31, e.g., from SEQ ID NO 308 and SEQ ID NO 325, respectively;
v of examples 22-24 and 52-54 H And V L The domains are from polypeptide 32, e.g., from SEQ ID NO 309 and SEQ ID NO 326, respectively;
v of examples 25-27 and 55-57 H And V L The domains are from polypeptide 33, e.g., from SEQ ID NO 310 and SEQ ID NO 337, respectively; and is also provided with
V of examples 28-30 and 58-60 H And V L The domains are derived from polypeptide 38, e.g., from SEQ ID NO. 315 and SEQ ID NO. 332, respectively.
Table 10.Car constructs
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Thus, provided herein are chimeric antigen receptors comprising the sequences disclosed in the following illustrative examples.
Table 11.Car sequence
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Similar CARs comprising scFv with variations are also possible.
For example, a CD34 tag may be associated with a P2A sequence (allowing forSo that they are co-expressed as discrete proteins) are included together in an expression vector, or (GGGGS) 4 Joint can be quilt (GGGGS) 3 、(GGGGS) 2 Or (GGGGS) 1 And (3) replacing the joint. For example, there is also provided:
CAR examples 1a-60a, which are identical to those above, except that they are accompanied by a CD34 tag;
CAR examples 1b-60b, which are identical to those above, except that they have (GGGGS) 3 A joint;
CAR examples 1c-60c, which are identical to those above, except that they have (GGGGS) 3 Linkers, and they accompany the CD34 tag;
CAR examples 1d-60d, which are identical to those above, except that they have (GGGGS) 2 A joint;
CAR examples 1e-60e, which are identical to those above, except that they have (GGGGS) 2 Linkers, and they accompany the CD34 tag;
CAR examples 1f-60f, which are identical to those above, except that they have a (GGGGS) linker; and
CAR examples 1g-60g, which are identical to those above, except that they have a (GGGGS) linker and they are accompanied by a CD34 tag.
Example 7: immune effector cells carrying CARs
Immune effector cells carrying CARs can be constructed, optionally using a genome editing step to achieve deletion or suppression of one or more surface proteins. Many of such surface proteins include, for example, those that form part of a TCR complex, which can induce GvHD if the cells are administered to a patient in an allogeneic setting; or those surface proteins that belong to the target antigen of the CAR, which can induce self-phase killing if the expression of the antigen on CAR-T is not suppressed.
For example, in one embodiment, on day 0, cd4+cd8+ T cells are thawed in cell culture medium. The desired number of cells were centrifuged at 200x g for 10 minutes at room temperature. The supernatant was completely removed and the cells were washed with 1X 10 6 The individual/ml concentrations were resuspended in cell culture medium (TexMacs) supplemented with IL-7 (10 ng/ml) and IL-15 (10 ng/ml). With Meitian gentle Co (Milt)enyi) research grade TransAct TM (10. Mu.l/ml) T cells were stimulated.
On day 1, the desired amount of the CAR-containing viral vector is added to the activated cells at the desired m.o.i. (multiplicity of infection). The cells and virus were mixed and returned to the incubator at 37 ℃.
Table 12.
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On day 3, activated cells were washed to remove stimulation.
If genome editing is desired, the cells are harvested and counted. The desired number of cells were centrifuged at 100x g for 10 minutes at room temperature. The supernatant was removed completely, the cells were resuspended in electroporation buffer (1 ml) (e.g. Maxcyte EP buffer) and transferred to a microcentrifuge tube and centrifuged at 100x g for 10 minutes at room temperature. The supernatant is completely removed and the cells are then washed with a desired concentration (e.g., 5x 10 7 Each/ml) was resuspended in electroporation buffer (e.g., maxCyte EP buffer).
Commercially available Cas9 protein (10 μg) and commercially synthesized gRNA (20 μg) were complexed for 10 minutes at room temperature.
Cells (100 μl) were transferred into tubes containing complexed Cas9/gRNA, gently mixed, and all material transferred into MaxCyte OC100 tubes. Thereafter, electroporation was started using the Maxcyte program Expanded T cell 2. Following this procedure, activated cells may be transferred to 10ml of pre-warmed medium and returned to the incubator for additional 7-12 days of expansion.
FACS analysis can be used to show the purity of CAR-transduced cells (CAR expression and target gene deletion).
Example 8: in vitro cell killing assay
Target AML cell lines are available from commercial suppliers (ATCC). Validation of target tables by FACS analysis Target cell genotypes were obtained and obtained by DNA sequencing. The cells were modified to express CBR-GFP (click beetle luciferase and green fluorescent protein). Jurkat cells (target negative) were engineered to overexpress CD33 binding to the CD90.1 marker G69 Variants or CD33 R69 Variants to enable differentiation in a target protein independent manner by FACS. Prior to FACS analysis, target cells were incubated for 24 hours with:
·CART33 ARG69 comprising a polypeptide comprising V disclosed in polypeptide number 6 H And V L Antigen recognition domain of domain, or
·CART33 GLY69 Comprising a polypeptide comprising V disclosed in polypeptide number 30 H And V L An antigen recognition domain of the domain; or alternatively
Positive control, variant non-specific CART33,
the ratio of effector to target cells ranges, for example, from E:T 2:1 to E:T 1:32. Absolute cell counts of viable target cells were quantified by flow cytometry (attune, absolute counts in defined volumes). Percent cytotoxicity was defined as the viable target relative to the tumor-only control. Data were analyzed using FlowJo V10.
The results are shown in fig. 4 and 5. CART33 ARG69 Effective killing of CD33 ARG69 Target but not kill CD33 GLY69 A target. CART33 GLY69 Effective killing of CD33 GLY69 Target but not kill CD33 ARG69 A target. CART33 kills CD33 ARG69 Target and CD33 GLY69 Both targets.
The above assays can be repeated with other CAR cells comprising the surrogate polypeptide and cells expressing the appropriate target, and can be altered according to methods known in the art; for example, different ratios of effector to target may be used. It is expected that in additional experiments of this type, cells expressing polymorphic selective CARS will kill cells expressing the selected target polymorphism.
For example, CART33 will kill the cd33+ target, but is associated with the CD33 genotype (CD 33 R69 Or CD33 G69 ) Irrespective of the fact that the first and second parts are. Expected CART-CD33 G69 Killing and killingCD33 G69 Targets (e.g. HL60, KG1a or Jurkat CD33 G69 ) But does not kill CD33 R69 Targets (e.g. TF1, THP1 or Jurkat CD33 R69 ). Expected CART-CD33 R69 Killing CD33 R69 Targets (e.g. TF1, THP1 or Jurkat CD33 R69 ) But does not kill CD33 G69 Targets (e.g. HL60, KG1a, jurkat CD 33) G69 )。
Similarly, cells expressing polymorphism selective CARS targeting the polymorphism of FLT3 and CLL1 will kill cells expressing the selected target polymorphism and will retain cells expressing the other polymorphism. CART-FLT3 will kill FLT3+ targets, but will be more robust to FLT3 genotype (FLT 3 T227 Or FLT3 M227 ) Irrespective of the fact that the first and second parts are. Expected CART-FLT3 M227 Killing FLT3 M227 Targets (e.g. Jurkat FLT3 M227 ) But does not kill FLT3 T227 Targets (e.g. Jurkat FLT3 T227 ). Expected CART-FLT3 T227 Killing FLT3 T227 Targets (e.g. Jurkat FLT3 T227 ) But does not kill FLT3 M227 Targets (e.g. Jurkat FLT3 M227 ). CART-CLL1 will kill cll1+ target, but will be identical to CLL1 genotype (CLL 1 K244 Or CLL1 Q244 ) Irrespective of the fact that the first and second parts are. Expected CART-CLL1 Q244 Killing CLL1 Q244 Targets (e.g. Jurkat CLL1 Q244 ) But does not kill CLL1 K244 Targets (e.g. Jurkat CLL1 K244 ). Expected CART-CLL1 K244 Killing CLL1 K244 Targets (e.g. Jurkat CLL1 K244 ) But does not kill CLL1 Q244 Targets (e.g. Jurkat CLL1 Q244 )。
Example 9: CAR-T active AML cell line xenograft model
Six to ten week old immunodeficient NOD.Cg-Prkdcsccid Il2rgtm1Wjl Tg (CMV-IL 3, CSF2, KITLG) 1Eav/MloySzJ (NSG-SGM 3) mice can be used in xenograft experiments of murine patient origin. Both male and female mice can be used in the experiment and randomly assigned to treatment groups.
Target AML cell lines are available from commercial suppliers (ATCC). Target expression was confirmed by FACS analysis and target cell genotypes were obtained by DNA sequencing. The cells were modified to express CBR-GFP (click beetle luciferase and green fluorescent protein).
Will be in an appropriate amount, e.g. 1x10, on day-7 6 Individual cells are implanted into mice, followed by infusion of an appropriate amount, e.g., 2x10, on day 0 6 Individual CAR-T cells and appropriate controls.
For example, CD33 may be used G69 AML cell line KG1a was implanted in mice and CD33 was used G69 CAR-T cells or CD33 R69 CAR-T cells, positive controls (CD 33 CAR-T cells), or negative controls (e.g., CAR negative T cells).
Tumor burden can be monitored weekly by bioluminescence imaging (BLI). Mice will be monitored for survival. Bone marrow can be extracted from mice and tumor burden assessed using FACS.
CART33 (positive control) would be expected to kill the cd33+ target to match the CD33 genotype (CD 33 R69 Or CD33 G69 ) Regardless, tumor burden is reduced and survival is prolonged. Expected CART-CD33 G69 Killing CD33 G69 Targets (e.g., HL60 or KG1 a), reduce tumor burden and extend survival of mice. CD33 R69 Targets (e.g. TF1, THP1 or Jurkat CD33 R69 ) Will not be CART-CD33 G69 Killing, and thus CART-CD33 G69 Does not provide survival advantages or reduce tumor burden. Expected CART-CD33 R69 Killing CD33 R69 Targets (e.g., TF1 or THP 1), reduce tumor burden and extend survival of mice. Expected CART-CD33 R69 Not kill CD33 G69 Targets (e.g. HL60 or KG1 a), and thus carrying CD33 G69 CART-CD33 in mice of the target cell line R69 Does not provide survival advantages or reduce tumor burden.
Example 10: humanized xenograft model of CAR-T active AML cell line
NOD.Cg-Prkdcsccid Il2rgtm1Wjl Tg (CMV-IL 3, CSF2, KITLG) 1Eav/MloySzJ (CD34+hu-NSG-SGM 3) mice implanted with human CD34+ hematopoietic stem cells can be used in patient-derived xenograft experiments. Both male and female mice can be used in the experiment and randomly assigned to treatment groups.
Mice were bled and the implanted human cells were genotyped using PCR-based sequencing to determine the phenotype of the polymorphic target.
Target AML cell lines are available from commercial suppliers (ATCC). Target expression was confirmed by FACS analysis and target cell genotypes were obtained by DNA sequencing. The cells were modified to express CBR-GFP (click beetle luciferase and green fluorescent protein).
At 8-10 weeks after CD34 cord blood implantation, an appropriate amount, e.g., 1X 10 6 The AML cells are implanted into mice and then infused with an appropriate amount, e.g., 2X 10, on day 0 6 Individual CAR-T cells and appropriate controls.
For example, CD33 may be used G69 Implantation of the AML cell line KG1a into humanized CD34+CD33 R69 In mice, use CD33 G69 CAR-T cells or CD33 R69 CAR-T cells, positive controls (CD 33 CAR-T cells), or negative controls (e.g., CAR negative T cells).
Tumor burden can be monitored weekly by bioluminescence imaging (BLI). The survival of mice can be monitored. Bone marrow can be extracted from mice and tumor burden assessed using FACS. CD33 expression on implanted cord blood-derived cells obtained from the blood, spleen and bone marrow of mice by FACS analysis. Erythrocytes were lysed using erythrocyte lysis buffer (Sigma Aldrich) and washed with ice-cold PBS. Samples for flow cytometry were prepared by resuspending the cells in staining buffer (PBS supplemented with 0.5% bovine serum albumin and 2mM EOTA) and incubating for 30min at 4 ℃ with a pre-titrated saturated dilution of the appropriate fluorescent dye-labeled monoclonal antibody. The data may be analyzed using FlowJo V10.
CART33 (positive control) would be expected to kill the cd33+ target to match the CD33 genotype (CD 33 R69 + or CD33 G69 ) Irrelevant, and reduced tumor burden, but also lost human engraftment of hematopoietic cells. Expected CART-CD33 G69 Killing CD33 G69 Targets (e.g. HL60 or KG1 a) and do not kill CD33 R69 The stem cells are implanted to extend survival by reducing tumor burden while maintaining human hematopoietic cells. Expected CART-CD33 R69 Killing CD33 R69 Targets (e.g. TF1, THP), andand does not kill CD33 G69 The stem cells are implanted to extend survival by reducing tumor burden while maintaining human hematopoietic cells. Mice with the same CD33 variant on AML and implanted stem cells would be expected to have reduced tumor burden but not be able to maintain human hematopoietic cells.
Example 11: patient-derived xenograft model of CAR-T activity.
Six to ten week old immunodeficient NOD.Cg-Prkdcsccid Il2rgtm1Wjl Tg (CMV-IL 3, CSF2, KITLG) 1Eav/MloySzJ (NSG-SGM 3) mice can be used in xenograft experiments of murine patient origin. Both male and female mice can be used in the experiment and randomly assigned to treatment groups.
Xenografts of human blood cancers (e.g., AML) can be obtained from a variety of sources known in the art, including, for example, the public xenograft resource library (Public Repository of Xenografts, PRoXe, www.PRoXe.org). Will be in an appropriate amount, e.g. 1x 10, on day-7 6 Individual cells are implanted into mice, followed by infusion of an appropriate amount, e.g., 2x 10, on day 0 6 Individual CAR-T cells and appropriate controls.
For example, CD33 may be used R69 AML xenografts were implanted in mice and CD33 was used G69 CAR-T cells or CD33 R69 CAR-T cells, or negative controls (e.g., CAR negative T cells).
Peripheral blood and spleen were analyzed by flow cytometry after two weeks, four weeks and six weeks following CAR-T infusion. Erythrocytes were lysed using erythrocyte lysis buffer (sigma aldrich) and washed with ice-cold PBS. Samples for flow cytometry were prepared by resuspending the cells in staining buffer (PBS supplemented with 0.5% bovine serum albumin and 2mM EDTA) and incubating for 30min at 4 ℃ with a pre-titrated saturated dilution of the appropriate fluorescent dye-labeled monoclonal antibody. The data may be analyzed using FlowJo V10.
Expected CD33 R69 CAR-T will kill the implanted CD33 R69 AML cells, reduced tumor burden and prolonged survival. Expected CD33 G69 CAR-T will not kill the implanted CD33 R69 AML cells, and does notMay provide survival advantages or reduce tumor burden. If the implanted AML is heterozygous, it expresses CD33 R69 And CD33 G69 Both of them are CD33 G69 CAR-T and CD33 R69 Both CAR-ts will effectively kill the implanted primary AML, extending the survival of mice.
Example 12: AML cell line in vitro CAR-NK Activity
Target AML cell lines are available from commercial suppliers (ATCC). Target expression was confirmed by FACS analysis and target cell genotypes were obtained by DNA sequencing.
For example, CD33 G69 AML cell lines (e.g., KG1a or HL 60) and CD33 R69 AML cell lines (e.g., TF1 or THP 1) can be cultured in vitro.
Will then be engineered to express against CD33 R69 NK cells of scFv-CAR added to CD33 cultured for 4-24 hours R69 Or CD33 G69 In cells. After incubation, CD33 is expected R69 Cell death will be enhanced while CD33 G69 Cell death will be no higher than background killing of unmodified NK cells. Is expected to be directed against CD33 G69 Will kill CD33 by scFv-CAR NK G69 Cells but not enhance CD33 R69 Killing of cells. As a positive control, an anti-CD 33 CAR can be used, while as a negative control, NK cells alone can be used.
Alternatively, NK cells may be present in CD33 R69 Or CD33 G69 In the case of AML cell lines and in the presence of a cell line with a targeted CD33 R69 Is cultured in the presence of an antibody of the human IgG1 or IgG3 isotype. After co-cultivation, death of AML cell lines will be assessed and CD33 is expected R69 AML cells have higher mortality. As a positive control, an anti-CD 33 antibody may be used, while as a negative control, NK cells alone may be used.
CARNK33 (positive control) is expected to kill CD33+ targets against the CD33 genotype of AML (CD 33) R69 Or CD33 G69 ) Irrespective of the fact that the first and second parts are. Contemplated CARNK-CD33 G69 Killing CD33 G69 Targets (e.g., HL60 or KG1 a). CD33 R69 Targets (e.g. TF1 or THP 1) not being affected by CARNK-CD33 G69 Killing, and thus in, the bodyCARNK-CD33 in an external assay G69 And not enhanced in this respect. Contemplated CARNK-CD33 R69 Killing CD33 R69 Targets (e.g., TF1 or THP 1). Contemplated CARNK-CD33 R69 Will not kill CD33 G69 Targets (e.g., HL60 or KG1 a), and thus CARNK-CD33 in this in vitro assay R69 And not enhanced in this respect.
Treatment comprising administration of NK cells with anti-CD 33 antibodies (positive control) is expected to kill cd33+ targets versus CD33 genotypes of AML (CD 33 R69 Or CD33 G69 ) Irrespective of the fact that the first and second parts are. Expected and anti-CD 33 G69 NK cell killing CD33 cultured with antibody G69 Targets (e.g., HL60 or KG1 a). CD33 R69 Targets (e.g., TF1 or THP 1) will not be conjugated to anti-CD 33 G69 NK cells cultured with antibodies kill, and thus target CD33 R69 In this assay of target cell lines, anti-CD 33 G69 NK cells administered with antibodies did not increase AML cell death. Expected and anti-CD 33 R69 NK cell killing CD33 with antibody administration R69 Targets (e.g., TF1 or THP 1). Expected and anti-CD 33 R69 NK cells cultured with antibodies did not kill CD33 G69 Targets (e.g., HL60 or KG1 a), and thus are directed against CD33 G69 In this assay of target cell lines, anti-CD 33 R69 NK cells administered with antibodies did not increase AML cell death.
Example 13: CAR-NK active AML cell line xenograft model
Six to ten week old immunodeficient NOD.Cg-Prkdcsccid Il2rgtm1Wjl Tg (CMV-IL 3, CSF2, KITLG) 1Eav/MloySzJ (NSG-SGM 3) mice can be used in xenograft experiments of murine patient origin. Both male and female mice can be used in the experiment and randomly assigned to treatment groups.
Target AML cell lines are available from commercial suppliers (ATCC). Target expression was confirmed by FACS analysis and target cell genotypes were obtained by DNA sequencing. The cells were modified to express CBR-GFP (click beetle luciferase and green fluorescent protein).
Will be in an appropriate amount, e.g. 1x10, on day-7 6 Individual cells were implanted into mice and subsequently infused on day 0By injecting appropriate amounts, e.g. 5x 10 6 Individual CAR-NK or NK cells and appropriate controls.
For example, CD33 may be used G69 AML cell line KG1a was implanted in mice and CD33 was used G69 CAR-NK cells or CD33 R69 CAR-NK cells, positive controls (CD 33 CAR-NK cells), or negative controls (e.g., CAR-negative NK cells).
Alternatively, CD33 may be used R69 AML cell line TF1 was implanted in mice and treated with: and against CD33 G69 Or CD33 R69 NK cells co-administered with antibodies of the human IgG1 or human IgG3 isotype, positive controls (NK cells and universal anti-CD 33 antibodies) or negative controls (e.g., NK cells only).
Tumor burden can be monitored weekly by bioluminescence imaging (BLI) and bone. Mice will be monitored for survival. Bone marrow can be extracted from mice and tumor burden assessed using FACS.
CARNK33 (positive control) is expected to kill CD33+ targets against the CD33 genotype of AML (CD 33) R69 Or CD33 G69 ) Regardless, tumor burden is reduced and survival is prolonged. Contemplated CARNK-CD33 G69 Killing CD33 G69 Targets (e.g., HL60 or KG1 a), reduce tumor burden and extend survival of mice. CD33 R69 Targets (e.g. TF1 or THP 1) not being affected by CARNK-CD33 G69 Killing, and thus CARNK-CD33 G69 Does not provide survival advantages or reduce tumor burden. Contemplated CARNK-CD33 R69 Killing CD33 R69 Targets (e.g., TF1 or THP 1), reduce tumor burden and extend survival of mice. Contemplated CARNK-CD33 R69 Not kill CD33 G69 Targets (e.g. HL60 or KG1 a), and thus carrying CD33 G69 CARNK-CD33 in mice of the target cell line R69 Does not provide survival advantages or reduce tumor burden.
Treatment comprising administration of NK cells with anti-CD 33 antibodies (positive control) is expected to kill cd33+ targets versus CD33 genotypes of AML (CD 33 R69 Or CD33 G69 ) Regardless, tumor burden is reduced and survival is prolonged. Expected and anti-CD 33 G69 NK cell killing CD33 with antibody administration G69 Targets (e.g. HL60 orKG1 a), reduces tumor burden and prolongs survival of mice. CD33 R69 Targets (e.g., TF1 or THP 1) will not be conjugated to anti-CD 33 G69 NK cells administered with antibodies kill, and thus are anti-CD 33 G69 NK cells administered with antibodies do not provide survival advantages or reduce tumor burden. Expected and anti-CD 33 R69 NK cell killing CD33 with antibody administration R69 Targets (e.g., TF1 or THP 1), reduce tumor burden and extend survival of mice. Expected and anti-CD 33 R69 NK cells administered with antibodies did not kill CD33 G69 Targets (e.g. HL60 or KG1 a), and thus carry CD33 G69 In mice of the target cell line, with anti-CD 33 R69 NK cells administered with antibodies do not provide survival advantages or reduce tumor burden.
Example 14: antibodies comprising scFv
Antibodies can be constructed from the scFv disclosed herein using methods known in the art. For example, the antibodies disclosed herein may be expressed from the form pFUSE IgG1 Fc fusion protein expression plasmid (e.g., invivogen Inc.)
I- - [ (leader) sequence (scFv V H )(hCγ1)(hCγ2)(hCγ3)(Cγs)]--|
Is produced from the expression cassette in the form of a pFUuse IgK Fc fusion protein expression plasmid (e.g.Invivogen)
I- - [ (leader) sequence (scFv V L )(hC κ/λ )]--|
Is produced by the expression cassette of (a).
Alternatively, an anti-CD 33-R69 or anti-CD 33-G69 antibody may be produced from an expression cassette of the form:
i- - [ (leader) sequence (scFv V H )(hCγ1)(hCγ2)(hCγ3)(Cγs)]-[P2A]- [ (leader sequence) (scFvV L )(C κ/λ )]-|。
In any of the foregoing cases, cγs can optionally be part of hcγ3 domain.
Antibodies may belong to various isotypes, the constant domains of which are known in the art. For example, for IgG1 or IgG4, the sequence components can be as shown in table 13:
TABLE 13 Fc component of human antibodies
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The foregoing may be combined with, for example, the following: v having the polypeptide sequence of any one of SEQ ID NOS 151-175 H V of a domain and/or polypeptide sequence having any one of SEQ ID NOs 176-200 L A domain; v having the polypeptide sequence of any one of SEQ ID NOs 303-319 H V of a domain and/or polypeptide sequence having any one of SEQ ID NOs 320 to 336 L A domain; v having the polypeptide sequence of any one of SEQ ID NOS 481-504 H V of a domain and/or polypeptide sequence having any of SEQ ID NOs 505 to 528 L A domain; or V having the polypeptide sequence of any one of SEQ ID NO 661-682 or the nucleotide sequence encoding any one of SEQ ID NO 661-682 H V domain and/or polypeptide sequence having any one of SEQ ID NOs 683-704 L A domain; or a nucleotide sequence encoding any of the foregoing.
Additional antibodies can be derived from V H And V L Domain construction, these domains are non-selective for a particular polymorphism. For example, the elements in table 13 may be combined with, for example, the following: v having the polypeptide sequence of any one of SEQ ID NOs 1035-1089 H V domain and/or polypeptide sequence having any one of SEQ ID NO 1090-1144 L A domain; or V having the polypeptide sequence of any one of SEQ ID NOS 1427-1473 H V of a domain and/or polypeptide sequence having any one of SEQ ID NOs 1474 to 1520 L A domain; or a nucleotide sequence encoding any of the foregoing.
Cloning vectors (e.g., plasmids) comprising sequences of the foregoing forms may be expressed in appropriate cell lines (e.g., 293F cells); transient transfection is typically sufficient. 293F cells were grown in FBS without IgG with agitation (e.g., roller bottles) and supernatants were harvested over the course of several (e.g., 5) days. The supernatant is purified using a protein a or G column and the antibodies recovered using methods known in the art.
Antibodies so produced may comprise VH and VL domains, as shown in table 14 below. Antibodies (mAbs) examples 1-42 target CD33 and examples 43-88 target CLL-1.
TABLE 14 IgG1 antibodies
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TABLE 15 IgG4 antibodies
Antibodies (mAbs) examples 89-130 target CD33 and examples 131-176 target CLL-1.
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Example 15: AML cell line xenograft model using antibody drug conjugates
Antibody drug conjugates can be produced by conjugating a biologically active compound to a variant specific antibody. Examples may include molecules such as saporin (ribosome inactivating protein), MMAE, MMAF, DM1 or DM4 and anti-CD 33 R69 Antibodies or anti-CD 33 G69 Conjugation of antibodies, which results in cell death following antigen binding and antibody-mediated drug internalization.
Six to ten week old immunodeficient NOD.Cg-Prkdcsccid Il2rgtm1Wjl Tg (CMV-IL 3, CSF2, KITLG) 1Eav/MloySzJ (NSG-SGM 3) mice can be used in xenograft experiments of murine patient origin. Both male and female mice can be used in the experiment and randomly assigned to treatment groups.
Target AML cell lines are available from commercial suppliers (ATCC). Target expression was confirmed by FACS analysis and target cell genotypes were obtained by DNA sequencing. The cells may be modified to express CBR-GFP (click beetle luciferase and green fluorescent protein).
Will be in an appropriate amount, e.g. 1x10, on day-7 6 Individual cells were implanted into mice. On day 0, mice are treated with an appropriate amount of ADC (e.g., in a dosage range of 0.1mg/kg to 5 mg/kg) on days 0, +7, and +14.
For example, CD33 may be used R69 AML cell line KG1a was implanted in mice and with anti-CD 33 G69 Saporin or anti-CD 33 R69 Saporin, positive control (anti-CD 33 saporin) or negative control (anti-CD 33 and saporin free) treatment.
Tumor burden can be monitored weekly by bioluminescence imaging (BLI). Mice will be monitored for survival. Bone marrow can be extracted from mice and tumor burden assessed using FACS.
It is expected that anti-CD 33-saporin (positive control) will kill the cd33+ target and bind to the CD33 genotype (CD 33) R69 Or CD33 G69 ) Regardless, tumor burden is reduced and survival is prolonged. anti-CD 33 is contemplated R69 Saporin killing CD33 R69 Targets (e.g., KG1 a), reduce tumor burden and extend survival of mice. anti-CD 33 is contemplated G69 Saporin does not kill CD33 R69 Targets, and do not provide survival advantages or reduce tumor burden.
Example 16: clinical application
Several clinical applications of polymorphic selective treatment of a subject are given below. In the following examples, the polymorphic antigen may be, for example, CD33, FLT3 or CLL-1; for purposes of illustration, CD33 will be used.
Scenario 1: no past screening, screening patients at recurrence. In this scenario, subjects with cancer (e.g., MDS or AML) are conditioned and transplanted with HSCs from related or unrelated histocompatibility donors, whether from the same sibling of Human Leukocyte Antigen (HLA), HLA-matched donors, umbilical cord blood units, or haploid donors, screened for low probability of allograft rejection and graft versus host disease (GvHD). Most HSCT receptors eventually relapse. If relapse occurs, the subject is eligible to receive therapy using polymorphic selective treatments such as CAR-bearing immune effector cells (e.g., TCR-deleted CAR-T or CAR-NK or CAR-iNKT), or NK cells in combination with antibodies that induce ADCC, which target antigens expressed on the surface of the malignant cells of the subject.
If the subject relapses after transplantation, the subject is genotyped using protein-based methods (e.g., FACS) or DNA-based methods (PCR) to ensure that the HSC donor and patient express different variants of the target antigen (e.g., CD 33). If the subject and donor do express different variants of the target antigen, e.g. one expressing CD33 R69 While the other expresses CD33 G69 The subject is eligible for polymorphism therapy. The subject is then conditioned (e.g., cyclophosphamide/fludarabine, 3 days) and treated with CAR-bearing immune effector cells (e.g., TCR-deleted CAR-T or CAR-NK or CAR iNKT), or NK cells in combination with antibodies that induce ADCC that target a patient-specific target antigen. For example, its cells express CD33 R69 And its HSCT graft expression is available with CD33 G69 Treated patients may use TCR-deleted CD33 R69 CART, or CD33 R69 anti-CD 33 of-CAR-NK, or donor NK cells, inducing ADCC R69 The combination of antibodies is treated. CD33 R69 The selective therapy will kill cancerous cells of the subject and retain expression of CD33 G69 Is a HSCT cell of (C). Combinations of reverse mismatches are also effective. The subject may then be monitored and optionally treated again with one or more of these selective therapies.
Scenario 2: prospective screening, screening patients on recurrence. In this scenario, HSCT donors are subjected to prospective screening to assess polymorphic variants of a given target antigen (e.g., CD 33) expressed by the donor, and identify donors expressing variants that differ from the intended recipient subject. This can be achieved by genotyping the patient and donor using a (PCR) -based genotyping method. At this point, HSCs and immune effector cells (e.g., T cells, NK cells, and iNKT cells) can be harvested from the same donor and isolated via leukopenia. HSCs can be used for transplantation into target mismatched recipients The method comprises the steps of carrying out a first treatment on the surface of the And immune effector cells can be used to selectively bind antigen variants (e.g., CD 33) expressed by cells of the recipient rather than the donor R69 Or CD33 G69 ) Or stored for later use if desired.
Conditioning the subject and transplanting with HSCs from a target mismatched donor, e.g., expressing CD33 G69 And it is used for expressing CD33 R69 Or vice versa. The donor may be a related or unrelated histocompatibility donor as described above.
If relapse occurs, the subject is conditioned (e.g., cyclophosphamide/fludarabine, 3 days) and treated with a polymorphic selective treatment such as CAR-bearing immune effector cells (e.g., CAR-T, CAR-NK or CAR-iNKT with CAR-T, TCR deleted), or NK cells in combination with antibodies that induce ADCC, which polymorphic selective treatment targets variants of antigens expressed on the malignant cell surface of the subject and not on the cell surface of the donor. For example, its cells express CD33 R69 And its HSCT graft expression is available with CD33 G69 Treated patients may use TCR-deleted CD33 R69 CART, or CD33 R69 anti-CD 33 of-CAR-NK, or donor NK cells, inducing ADCC R69 The combination of antibodies is treated. CD33 R69 Selective therapy would kill subjects expressing CD33 R69 And retain expression of CD33 G69 Is a HSCT cell of (C). Combinations of reverse mismatches are also effective. The subject may then be monitored and optionally treated again with one or more of these selective therapies.
Scenario 3: prospective screening and treating patients when recurrence occurs. In this scenario, HSCT donors are subjected to prospective screening to assess polymorphic variants of a given target antigen (e.g., CD 33) expressed by the donor, and identify donors expressing variants that differ from the intended recipient subject. This can be achieved by genotyping the patient and donor using a (PCR) -based genotyping method.
Conditioning the subject and transplanting with HSC from a target mismatched donor, which isFor example expressing CD33 G69 And it is used for expressing CD33 R69 Or vice versa. The donor may be a related or unrelated histocompatibility donor as described above. If recurrence occurs, the subject is conditioned (e.g., cyclophosphamide/fludarabine, 3 days) and treated with a polymorphic selective treatment such as CAR-bearing immune effector cells (e.g., TCR-deleted CAR-T, CAR-NK or CAR-iNKT), or a combination of NK cells and antibodies that induce ADCC, or antibody-drug conjugates comprising antibodies that induce ADCC, that targets variants of the antigen expressed on the malignant cell surface of the subject and not on the cell surface of the donor. For example, its cells express CD33 R69 And its HSCT graft expression is available with CD33 G69 Treated patients may use TCR-deleted CD33 R69 CART, or CD33 R69 anti-CD 33 of-CAR-NK, or donor NK cells, inducing ADCC R69 The combination of antibodies is treated. CD33 R69 Selective therapy would kill subjects expressing CD33 R69 And retain expression of CD33 G69 Is a HSCT cell of (C). Combinations of reverse mismatches are also effective. The subject may then be monitored and optionally treated again with one or more of these selective therapies.
Scenario 4: prospective screening, treatment at the time of transplantation. In this scenario, HSCT donors are subjected to prospective screening to assess polymorphic variants of a given target antigen (e.g., CD 33) expressed by the donor, and identify donors expressing variants that differ from the intended recipient subject. This can be achieved by genotyping the patient and donor using a (PCR) -based genotyping method.
Conditioning the subject and transplanting with HSCs from a target mismatched donor, e.g., expressing CD33 G69 And it is used for expressing CD33 R69 Or vice versa. The donor may be a related or unrelated histocompatibility donor as described above. Conditioning may be as standard HSCT (complete myeloablative) or Reduced Intensity Conditioning (RIC); or alternatively, may be a T cell depleted transplant.
Almost simultaneously with transplantation (i.e., within 1, 2, 3, or 10 days of HSCT, but in any case without requiring recurrence), subjects are treated with polymorphic selective treatments such as CAR-bearing immune effector cells (e.g., CAR-T, CAR-NK or CAR-iNKT with CAR-T, TCR deleted), or NK cells in combination with antibodies that induce ADCC, which selectively treat variants of antigens expressed on the malignant cell surface of the subject and not on the cell surface of the donor. For example, its cells express CD33 R69 And its HSCT graft expression is available with CD33 G69 Treated patients may use TCR-deleted CD33 R69 CART, or CD33 R69 anti-CD 33 of-CAR-NK, or donor NK cells, inducing ADCC R69 The combination of antibodies is treated. CD33 R69 Selective therapy would kill subjects expressing CD33 R69 And retain expression of CD33 G69 Is a HSCT cell of (C). Combinations of reverse mismatches are also effective. The subject may then be monitored and optionally treated again with one or more of these selective therapies.
The foregoing methods may be applicable to demonstrate binding and polymorphic selectivity of other scFv, antibodies, antibody-drug conjugates, and CARs to antigens such as cancer antigens. For example, these methods are expected to demonstrate that anti-FLT 3 scFv selectively binds to T227 or M227 variants. These methods are also expected to demonstrate that anti-CLL-1 scFv selectively binds either K244 or Q244 variants.
Example 17: identification of non-Selective anti-human CD33scFv clones
The method of example 1 above has been used to find polymorphic non-selective anti-human CD33scFv clones.
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Table 16b. Sequences of non-selective anti-CD 33 polypeptides (VH and VL sequences)
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The polypeptides described above were tested as disclosed in examples 4 and 5. The data are disclosed in table 16c below, which reports FACS fold changes to the parent as (-): indication < 2-fold; (+): indicating 2-10 times; (++): indicating 10-30 times; and [ (II) a ] ++ +): indicated >30 times.
TABLE 16c polypeptide Activity (FACS and BLI)
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Example 18: identification of non-Selective anti-human CLL-1scFv clones
The method of example 1 above has been used to find non-selective anti-human CLL-1scFv clones.
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TABLE 17b sequence of non-selective anti-CLL-1 polypeptide (VH and VL sequences)
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The polypeptides described above were tested as disclosed in example 4 above. The data are disclosed in table 17c below, which reports FACS fold changes to the parent as (-): indication < 2-fold; (+): indicating 2-10 times; (++): indicating 10-30 times; and [ (II) a ] ++ +): indicated >30 times.
TABLE 17c polypeptide Activity (FACS)
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Example 19: identification of non-Selective anti-human FLT 3scFv clones
The method in example 1 above has been used to find non-selective anti-human FLT 3scFv clones. Anti-human FLT-3scFv clones were found by standard screening methods of human antibody libraries using two recombinant polymorphic forms of the human FLT3 extracellular domain antigen (huFLT 3-T227 and huFLT 3-M227). Using these antigens, a variety of panning strategies are employed to facilitate enrichment of thermostable clones with the desired range of affinities. scFv were screened by flow cytometry and Biological Layer Interferometry (BLI) for binding to two Single Nucleotide Polymorphism (SNP) variants (threonine 227 and methionine 227) of human FLT-3.
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Table 18b. Sequences of non-Selective anti-FLT 3 polypeptides (VH and VL sequences)
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The polypeptides described above were tested as disclosed in examples 4 and 5. The data are disclosed in table 18c below, which reports FACS fold changes to the parent as (-): indication < 2-fold; (+): indicating 2-10 times; (++): indicating 10-30 times; and [ (II) a ] ++ +): indicated >30 times.
TABLE 18c polypeptide Activity (FACS and BLI)
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The detailed description set forth above is provided to assist those skilled in the art in practicing the present disclosure. However, the scope of the disclosure described and claimed herein is not limited by the specific embodiments disclosed herein, as these embodiments are intended to illustrate several aspects of the disclosure. Any equivalent embodiments are intended to be within the scope of this disclosure. Indeed, various modifications of the disclosure in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description without departing from the spirit or scope of the inventive concepts found herein. Such modifications are also intended to fall within the scope of the appended claims.

Claims (153)

1. A polypeptide that selectively binds to a first polymorphic variant of a human cancer cell antigen relative to a second polymorphic variant of the human cancer cell antigen; or a second polymorphic variant that selectively binds to the antigen relative to the first polymorphic variant of the antigen.
2. The polypeptide of claim 1, wherein the antigen is selected from CD33, CLL-1, and FLT3.
3. The polypeptide of claim 2, wherein the antigen is CD33.
4. A polypeptide that selectively binds to a first polymorphic variant of CD33 relative to a second polymorphic variant of CD 33; or a second polymorphic variant that selectively binds to the CD33 relative to the first polymorphic variant of the CD 33; wherein the binding has a selectivity of at least 2-fold.
5. The polypeptide of claim 4, wherein the binding is at least 10-fold selective.
6. The polypeptide of claim 5, wherein the binding has a selectivity of at least 30-fold.
7. The polypeptide of any one of claims 3-6, wherein the first polymorphic variant of CD33 is R69 and the second polymorphic variant of CD33 is G69; or the first polymorphic variant of CD33 is G69 and the second polymorphic variant of CD33 is R69.
8. The polypeptide of claim 7, comprising six Complementarity Determining Regions (CDRs).
9. The polypeptide of claim 8, comprising:
three heavy chain variable (V H ) Domain CDR: HCDR1, HCDR2 and HCDR3; and
three light chain variable (V L ) Domain CDR: LCDR1, LCDR2, and LCDR3.
10. The polypeptide of any one of claims 7-9, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1-25 and 201-217,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 26-50 and 218-234, and
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 51-75 and 235-251.
11. The polypeptide of any one of claims 7-9, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1-25,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 26-50, and
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 51-75.
12. The polypeptide of any one of claims 7-9, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 201-217,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 218-234, and
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 235-251.
13. The polypeptide of any one of claims 10-12, wherein the HCDR1, HCDR2 and HCDR3 have at least 97%, 98% or 99% sequence identity with one of said amino acid sequences.
14. The polypeptide of any one of claims 10-12, wherein the HCDR1, HCDR2 and HCDR3 have the amino acid sequence.
15. The polypeptide of any one of claims 7-14, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 76-100 and 252-268,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 101-125 and 269-285, and
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 126-150 and 286-302.
16. The polypeptide of any one of claims 7-14, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 76-100,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 101-125, and
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 126-150.
17. The polypeptide of any one of claims 7-14, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 252-268,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 269-285, and
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 286-302.
18. The polypeptide of any one of claims 15-17, wherein the LCDR1, LCDR2, and LCDR3 have at least 97%, 98%, or 99% sequence identity with one of the amino acid sequences.
19. The polypeptide of any one of claims 15-17, wherein the LCDR1, LCDR2, and LCDR3 have the amino acid sequence.
20. The polypeptide of claim 7, comprising V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 151-175 and 303-319.
21. The polypeptide of claim 7, comprising V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 151-175.
22. The polypeptide of claim 7, comprising V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 303-319.
23. The polypeptide of any one of claims 20-22, wherein the V H The domain has at least 97%, 98% or 99% sequence identity to one of the amino acid sequences.
24. The polypeptide of any one of claims 20-22, wherein the V H The domain has one of the amino acid sequences.
25. The polypeptide of any one of claims 7 and 20-24, comprising V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 176-200 and 320-336.
26. The polypeptide of any one of claims 7 and 20-24, comprising V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 176-200.
27. The polypeptide of any one of claims 7 and 20-24, comprising V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 320-336.
28. The polypeptide of any one of claims 25-27, wherein the V L The domain has at least 97%, 98% or 99% sequence identity to one of the amino acid sequences.
29. The method of any one of claims 25-27Wherein the V is L The domain has one of the amino acid sequences.
30. The polypeptide of any one of claims 20-29, comprising V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 1-42.
31. The polypeptide of any one of claims 20-29, comprising V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 1-25.
32. The polypeptide of any one of claims 20-29, comprising V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 26-42.
33. The polypeptide of any one of claims 29-32, wherein the V H Domain and the V L The domain has at least 97%, 98% or 99% sequence identity to one of the pair of amino acid sequences.
34. The polypeptide of claim 2, wherein the antigen is FLT3.
35. A polypeptide that selectively binds to a first polymorphic variant of FLT3 relative to a second polymorphic variant of FLT 3; or a second polymorphic variant that selectively binds to the FLT3 relative to the first polymorphic variant; wherein the binding has a selectivity of at least 2-fold.
36. The polypeptide of claim 35, wherein the binding has a selectivity of at least 10-fold.
37. The polypeptide of claim 36, wherein the binding has a selectivity of at least 30-fold.
38. The polypeptide of any one of claims 34-37, wherein the first polymorphic variant of FLT3 is T227 and the second polymorphic variant of FLT3 is M227; or the first polymorphic variant of FLT3 is M227 and the second polymorphic variant of FLT3 is T227.
39. The polypeptide of claim 2, wherein the antigen is CLL-1.
40. A polypeptide that selectively binds to a first polymorphic variant of CLL-1 relative to a second polymorphic variant of CLL-1; or a second polymorphic variant that selectively binds to CLL-1 relative to the first polymorphic variant; wherein the binding has a selectivity of at least 2-fold.
41. The polypeptide of claim 40, wherein the binding has a selectivity of at least 10-fold.
42. The polypeptide of claim 40, wherein the binding has a selectivity of at least 30-fold.
43. The polypeptide of any one of claims 39-42, wherein the first polymorphic variant of CLL-1 is K224 and the second polymorphic variant of CLL-1 is Q244; or the first polymorphic variant of CLL-1 is Q224 and the second polymorphic variant of CLL-1 is K244.
44. The polypeptide of claim 43, which comprises six Complementarity Determining Regions (CDRs).
45. The polypeptide of claim 44, comprising:
three heavy chain variable (V H ) Domain CDR: HCDR1, HCDR2 and HCDR3; and
three light chain variable (V L ) Domain CDR: LCDR1, LCDR2, and LCDR3.
46. The polypeptide of any one of claims 43-45, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 337-360 and 529-550,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 361-384 and 551-572, an
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 385-408 and 573-594.
47. The polypeptide of any one of claims 43-45, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 337-360,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 361-384, an
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 385-408.
48. The polypeptide of any one of claims 43-45, wherein:
HCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS: 529-550,
HCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 551-572, and
HCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 573-594.
49. The polypeptide of any one of claims 46-48, wherein the HCDR1, HCDR2 and HCDR3 have at least 97%, 98% or 99% sequence identity with one of said amino acid sequences.
50. The polypeptide of any one of claims 46-48, wherein the HCDR1, HCDR2 and HCDR3 have the amino acid sequence.
51. The polypeptide of any one of claims 43-50, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 409-432 and 595-616,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 433-456 and 617-638, and
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 457-480 and 639-660.
52. The polypeptide of any one of claims 43-50, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS 409-432,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS 433-456, an
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 457-480.
53. The polypeptide of any one of claims 43-50, wherein:
LCDR1 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NO:595-616,
LCDR2 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 617-638, an
LCDR3 comprises an amino acid sequence having at least 95% sequence identity to an amino acid sequence selected from SEQ ID NOS: 639-660.
54. The polypeptide of any one of claims 51-53, wherein the LCDR1, LCDR2, and LCDR3 have at least 97%, 98% or 99% sequence identity with one of said amino acid sequences.
55. The polypeptide of any one of claims 51-53, wherein the LCDR1, LCDR2, and LCDR3 have the amino acid sequence.
56. The polypeptide of claim 44, comprising V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 151-175 and 303-319.
57. The polypeptide of claim 44, comprising V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 151-175.
58. The polypeptide of claim 44, comprising V H Domain of V H The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 303-319.
59. The polypeptide of any one of claims 56-58, wherein the V H The domain has at least 97%, 98% or 99% sequence identity to one of the amino acid sequences.
60. The polypeptide of any one of claims 56-58, wherein the V H The domain has one of the amino acid sequences.
61. The polypeptide of any one of claims 44 and 56-60, comprising V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity to a sequence selected from any one of SEQ ID NOs 176-200 and 320-336.
62. The polypeptide of any one of claims 44 and 56-60, comprising V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 176-200.
63. The polypeptide of any one of claims 44 and 56-60, comprising V L Domain of V L The domain has an amino acid sequence exhibiting at least 95% sequence identity with a sequence selected from any one of SEQ ID NOs 320-336.
64. The polypeptide of any one of claims 61-63, wherein the V L The domain has at least 97%, 98% or 99% sequence identity to one of the amino acid sequences.
65. The polypeptide of any one of claims 61-63, wherein the V L The domain has one of the amino acid sequences.
66. The polypeptide of any one of claims 56-65, comprising V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 43-88.
67. The polypeptide of any one of claims 56-65, comprising V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 43-66.
68. The polypeptide of any one of claims 56-65, comprising V H Domain and V L A combination of domains, wherein the combination is selected from those described in polypeptide numbers 67-88.
69. The polypeptide of any one of claims 66-68, wherein the V H Domain and the V L DomainHas at least 97%, 98% or 99% sequence identity to one of said pairs of amino acid sequences.
70. A single chain variable fragment (scFv) comprising the polypeptide of any one of claims 1-69.
71. A monoclonal antibody (mAb) or antigen-binding fragment thereof comprising the polypeptide of any one of claims 1-69.
72. The mAb or antigen-binding fragment thereof of claim 71 wherein the mAb is of an IgG, igM, or IgA isotype.
73. The mAb or antigen-binding fragment thereof of claim 72 wherein the mAb is of the IgG1 isotype.
74. The mAb or antigen-binding fragment thereof of claim 72 wherein the mAb is of the IgG3 isotype.
75. The mAb or antigen-binding fragment thereof of claim 72 wherein the mAb is of the IgG4 isotype.
76. The mAb or antigen-binding fragment thereof of claim 72 wherein the mAb is human or humanized.
77. The mAb or antigen-binding fragment thereof of any one of claims 45-50, wherein the mAb comprises a sequence selected from the group consisting of SEQ ID NOs 1627-1978.
78. An antibody-drug conjugate (ADC) comprising the mAb or antigen-binding fragment thereof of any one of claims 71-78.
79. An ADC as recited in claim 52, having formula I:
Ab-(L-D) p
(I)
wherein:
ab is an antibody comprising the polypeptide of any one of claims 1-43, or the antibody of any one of claims 45-51, or an antigen-binding fragment of one of the foregoing;
l is a linker;
d is a drug; and is also provided with
p is from about 1 to about 20.
80. The ADC of claim 79, wherein D is selected from saporin, MMAE, MMAF, DM, and DM4.
81. A Chimeric Antigen Receptor (CAR) comprising an extracellular ligand binding domain comprising the polypeptide of any one of claims 1-69.
82. The CAR of claim 81, further comprising:
a. a hinge domain;
b. a transmembrane domain;
c. optionally, one or more co-stimulatory domains; and
d. cytoplasmic signaling domains.
83. The CAR of claim 82, wherein the hinge domain is selected from fcyriiia, CD8 a, CD28, and IgG1.
84. The CAR of claim 83, wherein the hinge domain is CD8 a.
85. The CAR of any one of claims 82-84, wherein the transmembrane domain is selected from the alpha, beta, or zeta chain of the T cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD9, CD16, CD22, CD33, CD37, CD64, CDs0, CD86, CD134, CD137, and CD154.
86. The CAR of claim 85, wherein the transmembrane domain is CD28.
87. The CAR of any one of claims 82-86, wherein the cytoplasmic signaling domain is selected from the group consisting of CD8, cd3ζ, cd3δ, cd3γ, cd3ε, CD22, CD32, DAP10, DAP12, CD66d, CD79a, CD79b, fcγriiy, fcγriii y, fcεri β, fcεri γ (FCERIG), fcrγ, fcrβ, and fcrε.
88. The CAR of claim 87, wherein the cytoplasmic signaling domain is cd3ζ.
89. The CAR of any one of claims 82-88, wherein one co-stimulatory domain is selected from the group consisting of 4-1BB, CD28, and ICOS.
90. The CAR of claim 89, wherein the co-stimulatory domain is CD28.
91. The CAR of claim 89, wherein the co-stimulatory domain is 4-1BB.
92. The CAR of claim 89, comprising two or more co-stimulatory domains.
93. The CAR of claim 89, wherein two of the co-stimulatory domains are CD28 and 4-1BB.
94. The CAR of claim 82, comprising a sequence selected from SEQ ID NOs 1539-1598.
95. A nucleotide sequence encoding the polypeptide, scFv, mAb or CAR of any one of claims 1-94.
96. A vector comprising the nucleotide sequence of claim 95.
97. The vector of claim 96, wherein the vector is a lentiviral vector.
98. The vector of claim 97, wherein the lentiviral vector comprises a VSVG domain.
99. An engineered immune effector cell expressing the CAR of any one of claims 81-94 on its cell surface.
100. The engineered immune effector cell of claim 99, wherein the engineered immune effector cell expresses on its cell surface:
A first polymorphic variant of a human cancer cell antigen; and
a CAR that is selective for a second polymorphic variant relative to a first polymorphic variant of the antigen.
101. The engineered immune effector cell of claim 99, wherein the cell is a primary cell.
102. The engineered immune effector cell of claim 99, wherein the cell is derived from:
-induced pluripotent stem cells (ipscs);
-cord blood;
-peripheral blood; or alternatively
Immortalized cell lines.
103. The engineered immune effector cell of claim 102, wherein the immortalized cell line is NK-92.
104. The engineered immune cell of any one of claims 99-103, wherein the cell is selected from the group consisting of a T cell, a Natural Killer (NK) cell, a constant natural killer T (iNKT) cell, a macrophage, and a dendritic cell.
105. The engineered immune effector cell of claim 104, wherein the cell is a T cell.
106. The engineered immune effector cell of claim 105, wherein the T cell is selected from inflammatory T-lymphocytes, cytotoxic T-lymphocytes, regulatory T-lymphocytes, or helper T-lymphocytes.
107. The engineered immune effector cell of claim 105, wherein the engineered immune effector cell lacks subunits of the T cell receptor complex.
108. The engineered immune effector cell of claim 107, wherein the subunit of the T cell receptor complex is selected from the group consisting of Tcra (TRAC), tcrp, tcrδ, tcrγ, cd3ε, cd3γ, cd3δ, and cd3ζ.
109. The engineered immune effector cell of any one of claims 105-108, wherein the engineered immune effector cell lacks a cell surface protein that is a target of the CAR.
110. The engineered immune effector cell of claim 104, wherein the engineered immune effector cell is an NK cell.
111. The engineered immune effector cell of claim 110, wherein the engineered immune effector cell is a memory-like (ML) NK cell.
112. The engineered immune effector cell of claim 111, wherein the engineered immune effector cell is a cytokine-induced memory-like (CIML) NK cell.
113. The engineered immune effector cell of claim 104, wherein the engineered immune effector cell is an iNKT cell.
114. A method of treating a subject in need thereof, the subject having a first polymorphic variant of an antigen on the surface of a target cell, the method comprising:
b. optionally, treating the subject with one or more conditioning regimens to deplete target cells of the subject carrying the first polymorphic variant of the antigen;
c. Administering to the subject:
-an engineered population of immune effector cells expressing a Chimeric Antigen Receptor (CAR) that selectively binds a first polymorphic variant of the antigen on the surface of the target cell; or alternatively
-a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell; or alternatively
-an antibody-drug conjugate (ADC) comprising a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell; and
d. administering to the subject a population of donor hematopoietic cells, a plurality of which comprise a second polymorphic variant of the antigen;
wherein administration of the hematopoietic cells and administration of the CAR-expressing cells, mAb, or ADC may be performed simultaneously, or sequentially in either order.
115. A method of immunotherapy of a human subject in need thereof, the subject having a first polymorphic variant of an antigen on the surface of a target cell, the method comprising:
a. optionally, treating the subject with one or more conditioning regimens to deplete target cells of the subject carrying the first polymorphic variant of the antigen;
b. Administering to the subject a population of donor hematopoietic cells, a plurality of which comprise a second polymorphic variant of the antigen; and
c. administering to the subject:
-an engineered population of immune effector cells expressing a Chimeric Antigen Receptor (CAR) that specifically binds a first polymorphic variant of the antigen on the surface of a target cell; or alternatively
-a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell; or alternatively
-an antibody-drug conjugate (ADC) comprising a monoclonal antibody (mAb) or antigen-binding fragment thereof, which mAb or antigen-binding fragment thereof selectively binds to a first polymorphic variant of the antigen on the surface of the target cell.
116. A method of treating a subject in need thereof, the subject having a first polymorphic variant of an antigen on the surface of a target cell, the method comprising:
a. administering to the subject:
-an engineered population of immune effector cells expressing a Chimeric Antigen Receptor (CAR) that binds to the antigen on the surface of the target cell; or alternatively
-a monoclonal antibody (mAb) that binds to the antigen on the surface of the target cell; or alternatively
-an antibody-drug conjugate (ADC) comprising a monoclonal antibody (mAb) that binds to the antigen on the surface of the target cell; and
b. optionally, treating the subject with one or more conditioning regimens to deplete target cells of the subject carrying the first polymorphic variant of the antigen;
c. administering to the subject:
-an engineered population of immune effector cells expressing a Chimeric Antigen Receptor (CAR) that selectively binds a first polymorphic variant of the antigen on the surface of the target cell; or alternatively
-a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell; or alternatively
-an antibody-drug conjugate (ADC) comprising a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell; and
d. administering to the subject a population of donor hematopoietic cells, a plurality of which comprise a second polymorphic variant of the antigen;
wherein administration of the hematopoietic cells and administration of the CAR-expressing cells, mAb, or ADC may be performed simultaneously, or sequentially in either order.
117. The method of any one of claims 114-116, wherein the subject is a human.
118. The method of any one of claims 114-117, wherein the binding has a selectivity of at least 2-fold.
119. The method of claim 118, wherein the binding has a selectivity of at least 10-fold.
120. The method of claim 119, wherein the binding has a selectivity of at least 30-fold.
121. The method of any one of claims 114-120, wherein the antigen is selected from CD33, CLL-1, and FLT3.
122. The method of claim 121, wherein the antigen is CD33.
123. The method of claim 122, wherein the first polymorphic variant of CD33 is R69 and the second polymorphic variant of CD33 is G69; or the first polymorphic variant of CD33 is G69 and the second polymorphic variant of CD33 is R69.
124. The method of claim 121, wherein the antigen is FLT3.
125. A method according to claim 124, wherein the first polymorphic variant of FLT3 is T227 and the second polymorphic variant of FLT3 is M227; or the first polymorphic variant of FLT3 is M227 and the second polymorphic variant of FLT3 is T227.
126. The method of claim 121, wherein the antigen is CLL-1.
127. The method of claim 126, wherein the first polymorphic variant of CLL-1 is K224 and the second polymorphic variant of CLL-1 is Q244; or the first polymorphic variant of CLL-1 is Q224 and the second polymorphic variant of CLL-1 is K244.
128. The method of any one of claims 114-127, wherein the subject is administered both the engineered immune effector cell population and the hematopoietic cell population simultaneously.
129. The method of any one of claims 114-127, wherein the hematopoietic cell population, and the engineered immune effector cell population, mAb, or ADC are sequentially administered to the subject.
130. The method of any one of claims 114-127, wherein the population of engineered immune effector cells, mabs or ADCs, and the population of hematopoietic cells are sequentially administered to the subject.
131. The method of any one of claims 114-130, wherein prior to administration of the hematopoietic cells, the subject is treated with one or more conditioning protocols to deplete the subject of target cells bearing the first polymorphic variant of the antigen.
132. The method of any one of claims 114-130, wherein the subject has been conditioned with one or more conditioning protocols to deplete target cells of the subject that carry the first polymorphic variant of the antigen.
133. The method of any one of claims 114-132, wherein the hematopoietic cells are hematopoietic stem cells and/or hematopoietic progenitor cells.
134. The method of any one of claims 114-133, wherein the subject is administered an engineered population of immune effector cells expressing a Chimeric Antigen Receptor (CAR) that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell.
135. The method of claim 134, wherein the engineered immune effector cells are derived from the subject (i.e., autologous) and the hematopoietic cells are derived from a donor (i.e., allogeneic).
136. The method of claim 134, wherein the engineered immune effector cells and hematopoietic cells are derived from a single donor.
137. The method of claim 108, wherein the engineered immune effector cells are derived from a first donor and hematopoietic cells are derived from a second donor.
138. The method of any one of claims 134-137, wherein the Chimeric Antigen Receptor (CAR) comprises the polypeptide of any one of claims 1-69.
139. The method of any one of claims 134-137, wherein the Chimeric Antigen Receptor (CAR) comprises the scFv of claim 70.
140. The method of any one of claims 134-137, wherein the Chimeric Antigen Receptor (CAR) is the CAR of any one of claims 81-94.
141. The method of any one of claims 134-137, wherein the engineered immune effector cell is the engineered immune effector cell of any one of claims 99-113.
142. The method of any one of claims 114-133, wherein the subject is administered a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell.
143. The method of claim 142, wherein the monoclonal antibody (mAb) comprises the polypeptide of any one of claims 1-69.
144. The method of claim 142, wherein the monoclonal antibody (mAb) is a mAb of any one of claims 71-77.
145. The method of any one of claims 114-133, wherein an antibody-drug conjugate (ADC) comprising a monoclonal antibody (mAb) or antigen-binding fragment thereof that selectively binds to a first polymorphic variant of the antigen on the surface of the target cell is administered to the subject.
146. The method of any one of claims 142-145, wherein the mAb or ADC is administered prophylactically after transplantation to prevent relapse.
147. The method of any one of claims 114-146, further comprising genotyping the subject and donor to ensure that the HSC donor and patient express different variants of the target antigen.
148. The method of claim 147, wherein the genotyping is performed using a protein-based assay (FACS) or a DNA-based assay (PCR).
149. The method of claim 147, wherein the patient is genotyped after a recurrence of the transplant.
150. The method of claim 147, wherein the patient is genotyped prior to transplantation.
151. The method of claim 147, wherein the hematopoietic cell donor is genotyped prior to hematopoietic cell transplantation.
152. The method of any one of claims 137-147, wherein the immune effector cell donor is genotyped prior to transplanting an engineered immune effector cell population expressing the CAR.
153. The method of any one of claims 137-147, wherein the immune effector cell donor is genotyped prior to hematopoietic cell transplantation.
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